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How many subunits make up the RNA polymerase I complex in Arabidopsis thaliana? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis, RNA Pol I consists of 12 protein subunits common to RNA Pol II and Pol III the two others being RNA Pol I-specific subunits.",
"In Arabidopsis, RNA Pol I consists of 14 protein subunits: 12 are RNA Pol I-specific protein subunits and two others are common to RNA Pol II and Pol III.",
"In Arabidopsis, RNA Pol I consists of 12 subunits common to those of all nuclear RNA polymerases (RNA Pol I–Pol V). 5 are common to RNA Pol II and Pol III and the others are RNA Pol I-specific subunits."
] | 10.1093/nar/gkv247 | Model Organisms | GENE REGULATION | 10.1093/nar/gkv247 | 2,015 | 20 | 2 | Nucleic Acids Research | true |
What is in an RNA polymerase I holoenzyme? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"RNA Pol I holoenzyme is the RNA Pol I complex that associates with additional General Transcription Factor (GFTs) to form larger RNA Pol I complexes which are competent for RNA pol I elongation",
"RNA Pol I holoenzyme is the RNA Pol I “core” complex competent to specifically initiate rDNA transcription",
"The RNA Pol I holoenzyme is the RNA Pol I complex associated to General Transcription Factors (GFTs) to form larger RNA Pol I complexes capable of specifically initiating rDNA transcription"
] | 10.1073/pnas.94.22.11869 | Non-specific | GENE REGULATION | 10.1073/pnas.94.22.11869 | 1,997 | 48 | 2 | Proceedings of the National Academy of Sciences | true |
Can the activity of RNA polymerase I complex be regulated by casein kinase 2 (CK2)? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"CK2 interacts with the RNA Pol I holoenzyme and it can phosphorylate transcription factors, thereby increasing rDNA transcription",
"CK2-like protein (CASEIN KINASE2) interacts with the RNA Pol I holoenzyme and can desphosphorylate transcription factors, thereby increasing rDNA transcription.",
"CK2-like protein (CASEIN KINASE2) interacts with the RNA Pol I holoenzyme and can phosphorylate transcription factors, thereby decreasing rDNA transcription."
] | 10.1023/a:1011619413393 | Non-specific | GENE REGULATION | 10.1023/a:1011619413393 | 2,001 | 16 | 0 | Plant Molecular Biology | true |
Which genes are transcribed by RNA polymerase I in Arabidopsis plants? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"The RNA Pol I transcribes a single 45S rDNA copy gene encoding the rRNA 18S, 5.8S and 25S.",
"The RNA Pol I transcribes the rRNA 18S, 5.8S, 5S and 25S ",
"The RNA Pol I transcribes the tandemly organised 45S rDNA encoding the rRNA 18S, 5.8S and 25S. "
] | 10.1105/tpc.18.00874 | Model Organisms | GENE REGULATION | 10.1105/tpc.18.00874 | 2,019 | 124 | 2 | The Plant Cell | true |
Where does RNA polymerase I transcriptional activity take place? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"The RNA Pol I transcription takes place in the nucleolus and more precisely in the dense fibrillary centres (DFC).",
"The RNA Pol I transcription takes place in the nucleolus and more precisely in the dense fibrillary component (DFC).",
"The RNA Pol I transcription takes place in the nucleoplasm and more precisely in the dense fibrillary component (DFC)."
] | 10.1038/s41580-020-0272-6 | Non-specific | GENE REGULATION | 10.1038/s41580-020-0272-6 | 2,020 | 708 | 1 | Nature Reviews Molecular Cell Biology | true |
Can plant microRNA (miRNA) precursors be shortened to express artificial microRNAs (amiRNAs) from viral vectors? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Yes, plant miRNA precursors can be shortened to express amiRNAs from viral vectors, as such minimal precursors retain the essential structural features necessary for accurate processing and function.",
"No, plant miRNA precursors cannot be shortened to express amiRNAs from viral vectors, as such minimal precursors do not retain the essential structural features necessary for accurate processing and function.",
"Yes, plant miRNA precursors can be shortened to express artificial miRNAs from viral vectors, but the shortening removes essential structural features required for proper processing, resulting in non-functional amiRNAs."
] | https://doi.org/10.1093/nar/gkad747 | Non-specific | PLANT BIOTECHNOLOGY | 10.1093/nar/gkad747 | 2,023 | 16 | 0 | Nucleic Acids Research | true |
Can TAS1c-based synthetic trans acting small interfering RNAs (syn-tasiRNAs) move throughout Nicotiana benthamiana and induce the systemic silencing of the SULPHUR gene? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"No, TAS1c-based syn-tasiRNAs can move throughout Nicotiana benthamiana, but they are unable to induce systemic silencing of the SULPHUR gene because their movement is restricted to the local tissue where they are produced and do not enter the phloem for long-distance movement.",
"Yes, TAS1c-based syn-tasiRNAs can move throughout Nicotiana benthamiana and induce the systemic silencing of the SULPHUR gene. Syn-tasiRNAs are processed from TAS1c precursors and move as duplexes though the phloem to reach apical tissues where they are incorporated into ARGONAUTE1 proteins to degrade SULPHUR mRNAs.",
"Yes, TAS1c-based syn-tasiRNAs can move throughout Nicotiana benthamiana and induce the systemic silencing of the SULPHUR gene. TAS1c precursors move through the phloem to reach apical tissues where they are processed into syn-tasiRNA duplexes, and are incorporated into ARGONAUTE1 proteins to degrade SULPHUR mRNAs."
] | https://onlinelibrary.wiley.com/doi/10.1111/tpj.15730 | Non-specific | PLANT BIOTECHNOLOGY | 10.1111/tpj.15730 | 2,022 | 10 | 1 | The Plant Journal | true |
Under which molecular form do artificial microRNAs (amiRNAs) and synthetic trans acting small interfering RNAs (syn-tasiRNAs) move throughout Nicotiana benthamiana to induce systemic silencing of endogenous genes? | PLANT BIOTECHNOLOGY | [
"Nicotiana benthamiana"
] | [
"AmiRNAs and syn-tasiRNAs move throughout the plant to induce systemic silencing, typically in the form of ARGONAUTE 1-small RNA complexes that are ready for target-specific silencing.",
"AmiRNAs and syn-tasiRNAs move throughout the plant to induce systemic silencing, typically in the form of small RNA precursors that, in distal tissues, are processed into small RNA duplexes that are loaded into ARGONAUTE 1 for target-specific silencing.",
"AmiRNAs and syn-tasiRNAs move throughout Nicotiana benthamiana to induce systemic silencing, typically in the form of small RNA duplexes that are loaded into ARGONAUTE 1 for target-specific silencing."
] | https://onlinelibrary.wiley.com/doi/10.1111/tpj.15730 | Solanaceae & Relatives | PLANT BIOTECHNOLOGY | 10.1111/tpj.15730 | 2,022 | 10 | 2 | The Plant Journal | true |
Does multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs (syn-tasiRNAs) enhance plant antiviral resistance? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Yes, multi-targeting of viral RNAs with syn-tasiRNAs enhances plant antiviral resistance. By expressing multiple syn-tasiRNAs from a single precursor, plants can simultaneously target several regions of a viral genome or even multiple viral genomes, minimizing the likelihood of viral escape mutants, as the virus would need to mutate multiple target sites simultaneously to overcome the resistance.",
"No, multi-targeting of viral RNAs with syn-tasiRNAs fails to enhance plant antiviral resistance. Expressing multiple syn-tasiRNAs from a single precursor results in competition among the syn-tasiRNAs, reducing their overall efficiency and allowing viruses to evade silencing more easily.",
"Yes, multi-targeting of viral RNAs syn-tasiRNAs enhances plant antiviral resistance. By expressing multiple syn-tasiRNAs from a single precursor, plants can simultaneously target several regions of a viral genome or even multiple viral genomes, maximizing the likelihood of viral escape mutants, as the virus would not need to mutate multiple target sites simultaneously to overcome the resistance."
] | https://onlinelibrary.wiley.com/doi/10.1111/tpj.14466 | Non-specific | PLANT BIOTECHNOLOGY | 10.1111/tpj.14466 | 2,019 | 44 | 0 | The Plant Journal | true |
How is it possible to fine-tune control target RNAi efficacy in Arabidopsis thaliana using syn-tasiRNAs? | PLANT BIOTECHNOLOGY | [
"Arabidopsis thaliana"
] | [
"It is possible to fine-tune target gene expression with syn-tasiRNAs in Arabidopsis thaliana through two strategies: i) by modulating the level of accumulation of a syn-tasiRNA if changing its precursor position, and ii) by modifying the degree of base-pairing between the 3' end of the syn-tasiRNA and the 5' end of the target RNA.",
"It is possible to fine-tune target gene expression with syn-tasiRNAs in Arabidopsis thaliana through two strategies: i) by modulating the level of accumulation of a syn-tasiRNA if changing its precursor position, and ii) by modifying the degree of base-pairing between the 5' end of the syn-tasiRNA and the 3' end of the target RNA.",
"It is possible to fine-tune target gene expression with syn-tasiRNAs in Arabidopsis thaliana through two strategies: i) by modulating the level of accumulation of a syn-tasiRNA if maintaining its precursor position, and ii) by maintaining the degree of base-pairing between the 3' end of the syn-tasiRNA and the 5' end of the target RNA."
] | https://doi.org/10.1093/nar/gkaa343 | Model Organisms | PLANT BIOTECHNOLOGY | 10.1093/nar/gkaa343 | 2,020 | 20 | 0 | Nucleic Acids Research | true |
Do you find rna polymerase ii transcription start sites only in annotated gene promoter regions? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"No, there are two places where rna polymerase ii can start transcription. 1.) in gene promoters, 2.) in some regions between annotated genes. ",
"Yes, the only location where transcription starts are gene promoters. ",
"No, it is possible to detect transcription start sites in additional regions without annotated promoters, for example some intergenic regions. In addition, transcription can start within annotated genes on the sense and antisense strand. "
] | 10.1371/journal.pgen.1007969 | Non-specific | GENE REGULATION | 10.1371/journal.pgen.1007969 | 2,019 | 72 | 2 | PLOS Genetics | true |
Are plant genes are only transcribed in one direction? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"Yes, the only way plant genes can be transcribed is in the direction that results in sense mRNA. ",
"No, but the only type of antisense transcription from genes starts in the 3´-UTR of plant genes. ",
"No, antisense transcription is common. It can either be antisense transcription initiating in the 3´-UTR, or initiation of antisense transcription intragenically. "
] | 10.1093/nar/gkz1189 | Non-specific | GENE REGULATION | 10.1093/nar/gkz1189 | 2,019 | 91 | 2 | Nucleic Acids Research | true |
When transcription starts in gene promoters, are only possible outcomes the production of mRNA isoforms? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"No, rna polymerase ii can continue transcription of a different chromosome due to the 3-dimensional genome architecture of plants. ",
"Yes, once rna polymerase ii initiates transcription from a plant gene promoter the only outcome is the production of mRNA isoforms. ",
"No, initiation of rna polymerase ii transcription from gene promoters often results in the production of short promoter-proximal RNAs. "
] | 10.1038/s41467-020-16390-7 | Model Organisms | GENE REGULATION | 10.1038/s41467-020-16390-7 | 2,020 | 49 | 2 | Nature Communications | true |
Are there methylation signatures of histone H3 tails that correlate positively with rna polymerase ii transcriptional activity? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"non-specific"
] | [
"Yes, in particular tri-methylation and di-methylation of histone 3 lysine 4, and histone 3 lysine 36. ",
"Yes, histone 3 lysine 27 tri-methylation.",
"No, only acetylation of histone H3 tails correlates positively with rna polymerase ii transcription. "
] | 10.1016/j.tplants.2020.03.005 | Non-specific | GENE REGULATION | 10.1016/j.tplants.2020.03.005 | 2,020 | 33 | 0 | Trends in Plant Science | true |
Is the transcript resulting from the torpedo-mechanism of transcriptional termination is incorporated into standard genome annotations? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"No, standard methods such as RNA-seq usually rely on 3´- poly-adenylated and 5´-m7G capped RNA species. The transcript associated with torpedo termination lacks both of these features and is therefore usually missing in genome annotations unless the information from suitable methods is used. ",
"No, the reason is that these transcripts do not really exist because RNA-seq cannot detect them. ",
"Yes, these transcripts are generated when an mRNA is produced and are therefor also part of genome annotations. "
] | 10.1186/s12859-021-04259-5. | Non-specific | GENE REGULATION | 10.1186/s12859-021-04259-5 | 2,021 | 1 | 0 | BMC Bioinformatics | true |
How does the UV-B photoreceptor UVR8 regulate gene expression changes in Arabidopsis thaliana plants? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"After UV-B absorption, the homodimeric UVR8 induces its monomerization, and monomeric UVR8 interacts with the E3 ubiquitin ligases RUP1 and RUP2, leading to gene expression changes. UVR8 is then inactivated through redimerization, facilitated by COP1.",
"After UV-B absorption, the monomeric UVR8 induces its dimerization, and UVR8 dimers interact with the E3 ubiquitin ligase COP1, leading to gene expression changes. UVR8 is then inactivated through remonomerization, facilitated by RUP1 and RUP2.",
"After UV-B absorption, the homodimeric UVR8 induces its monomerization, and monomeric UVR8 interacts with the E3 ubiquitin ligase COP1, leading to gene expression changes. UVR8 is then inactivated through redimerization, facilitated by RUP1 and RUP2."
] | https://doi.org/10.1073/pnas.2017284118 | Model Organisms | ENVIRONMENT | 10.1073/pnas.2017284118 | 2,021 | 34 | 2 | Proceedings of the National Academy of Sciences | true |
Which are the similitudes and differences between palisade and other photosynthetic cells from Arabidopsis leaves exposed to UV radiation? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"Palisade cells have a unique morphology, but are transcriptionally similar to other photosynthetic cell types. However, some genes in the phenylpropanoid biosynthesis pathway, which are required for production of the ultraviolet protectant sinapoylmalate, have palisade-enriched expression. ",
"Palisade cells have a similar morphology, but are transcriptionally different to other photosynthetic cell types. Moreover, some genes in the phenylpropanoid biosynthesis pathway, which are required for production of the ultraviolet protectant sinapoylmalate, have palisade-enriched expression. ",
"Palisade cells have a unique morphology, and are transcriptionally different to other photosynthetic cell types. Moreover, some genes in the phenylpropanoid biosynthesis pathway, which are required for production of the ultraviolet protectant sinapoylmalate, have palisade-enriched expression. "
] | doi: 10.1093/plcell/koac167. | Model Organisms | ENVIRONMENT | 10.1093/plcell/koac167 | 2,022 | 60 | 0 | The Plant Cell | true |
Which proteins physically interact in the regulation of UV-B tolerance depending on the jasmonic acid signaling pathway in A. thaliana? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"UV RESISTANCE LOCUS 8 (UVR8), TEOSINTE BRANCHED1, Cycloidea and PCF 4 (TCP4) and LIPOXYGENASE2 (LOX2) physically interacts in the nuclei to increase the DNA binding activity of TCP4 and upregulate the JA biosynthesis.",
"UV RESISTANCE LOCUS 8 (UVR8) and TEOSINTE BRANCHED1, Cycloidea and PCF 4 (TCP4) physically interacts in the nuclei to increase the DNA binding activity of TCP4 and upregulate the JA biosynthesis gene LOX2.",
"UV RESISTANCE LOCUS 8 (UVR8), TEOSINTE BRANCHED1, Cycloidea and PCF 4 (TCP4) and LIPOXYGENASE2 (LOX2) physically interacts in the nuclei to increase the DNA binding activity of TCP4 and downregulate the JA biosynthesis."
] | https://doi.org/10.1111/jipb.13648 | Model Organisms | ENVIRONMENT | 10.1111/jipb.13648 | 2,024 | 9 | 1 | Journal of Integrative Plant Biology | true |
Which plant photoreceptors participate in the induction of FERULIC ACID 5-HYDROXYLASE 1 (FAH1), leading to the accumulation of UV-absorbing sinapate esters in Arabidopsis? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"Both UV RESISTANCE LOCUS 8 (UVR8) UV-B and phytochrome red, but not cryptochrome blue-light photoreceptors, converge on the induction of FERULIC ACID 5-HYDROXYLASE 1 (FAH1), which encodes a key enzyme in the phenylpropanoid biosynthesis pathway. This induction leads to the accumulation of UV-absorbing sinapate esters in Arabidopsis.",
"Both UV RESISTANCE LOCUS 8 (UVR8) UV-B and cryptochrome blue, but not phytochrome red light photoreceptors, converge on the induction of FERULIC ACID 5-HYDROXYLASE 1 (FAH1), which encodes a key enzyme in the phenylpropanoid biosynthesis pathway. This induction leads to the accumulation of UV-absorbing sinapate esters in Arabidopsis.",
"UV RESISTANCE LOCUS 8 (UVR8) UV-B, phytochrome red, and cryptochrome blue-light photoreceptors converge on the induction of FERULIC ACID 5-HYDROXYLASE 1 (FAH1), which encodes a key enzyme in the phenylpropanoid biosynthesis pathway. This induction leads to the accumulation of UV-absorbing sinapate esters in Arabidopsis."
] | https://doi.org/10.1093/plphys/kiae352 | Model Organisms | ENVIRONMENT | 10.1093/plphys/kiae352 | 2,024 | 1 | 2 | Plant Physiology | true |
What is the role of the Jumonji27 (JMJ27) protein during the UV-induced DNA damage in Arabidopsis thaliana plants? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"JMJ27 is responsible for the UV-induced reduction of H3K9me2 content at chromocenters. In addition, JMJ27 forms a complex with the photodamage recognition factor, DNA Damage Binding protein 2 (DDB2). The fine tuning of H3K9me2 contents orchestrates DDB2 dynamics on chromatin in response to UV-C exposure.",
"JMJ27 is responsible for the UV-induced increase in H3K9me2 content at chromocenters. In addition, JMJ27 forms a complex with the photodamage recognition factor, DNA Damage Binding protein 1 (DDB1). The fine tuning of H3K9me2 contents orchestrates DDB1 dynamics on chromatin in response to UV-C exposure.",
"JMJ27 is responsible for the UV-induced reduction in H3K9me2 content at chromocenters. In addition, JMJ27 forms a complex with the photodamage recognition factor, DNA Damage Binding protein 1 (DDB1). The fine tuning of H3K9me2 contents orchestrates DDB1 dynamics on chromatin in response to UV-C exposure."
] | https://doi.org/10.1038/s41477-024-01814-9 | Model Organisms | ENVIRONMENT | 10.1038/s41477-024-01814-9 | 2,024 | 1 | 0 | Nature Plants | true |
Which proteins have been identified as physical interactors of the C subunit of the Nuclear Factor Y 1 (NF-YC1) from common bean (Phaseolus vulgaris)? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Phaseolus vulgaris"
] | [
"SIN1 and NF-YA1 have been identified by bimolecular fluorescence complementation using an NF-YC1-gfp fusion. Both proteins are involved in nodule development. ",
"SIN1 and NIPK have been identified by a yeast two hybrid screening using NF-YC1 as a bait. Both proteins are involved in nodule development. ",
"SIN1 and NF-YA1 have been identified by a yeast two hybrid screening using NF-YC1 as a bait. Only NF-YA1 is involved in nodule development. "
] | 10.3389/fpls.2022.992543 10.1104/pp.113.230896 | Legumes | ENVIRONMENT | 10.1104/pp.113.230896 | 2,014 | 53 | 1 | Plant Physiology | true |
The promotor of which gene is recognized by the complex that contains NF-YC1 from common bean (Phaseolus vulgaris) and what is its function? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Phaseolus vulgaris"
] | [
"NF-YC1 binds to the promoter of Aurora, a cyclin protein that controls the cell cycle and is involved in root hair development",
"NF-YC1 binds to the promoter of the cyclin P3;1, a cyclin protein that controls the DNA repair and is involved in root hair development",
"NF-YC1 binds to the promoter of the cyclin P4;1,a cyclin protein that controls the cell cycle and is involved in nodule organogenesis"
] | https://doi.org/10.1111/nph.19419 | Legumes | ENVIRONMENT | 10.1111/nph.19419 | 2,023 | 0 | 2 | New Phytologist | true |
How small GTPases from the Rab subfamily have been associated to nodulation in common bean (Phaseolus vulgaris)? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Phaseolus vulgaris"
] | [
"RabA2a from common bean was identified by its differential expression in response to two different strains of Rhizobium leguminosarum. It is expressed in roots, particularly in athrichoblasts and the protein is located in vesicles. Genetic studies have shown that RabA2a is required for root growth, early infection events and nodule development.",
"RabA2a from common bean was identified by its differential expression in response to two different strains of Rhizobium etli. It is expressed in roots, particularly in thrichoblasts and the protein is located in vesicles. Genetic studies have shown that RabA2a is required for root hair growth, early infection events and nodule development.",
"RabA2a from common bean was identified by its differential expression in response to two different strains of Rhizobium tropici. It is expressed in roots, particularly in athrichoblasts and the protein is located in the nucleus. Genetic studies have shown that RabA2a is required for lateral root growth, early infection events and nodule development."
] | 10.1094/MPMI, 10.1105/tpc.108.063420 | Legumes | ENVIRONMENT | 10.1105/tpc.108.063420 | 2,009 | 51 | 1 | The Plant Cell | true |
How the trimer of NF-YC that acts during symbiosis was identified in common bean (Phaseolus vulgaris)? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Phaseolus vulgaris"
] | [
"The subunits of the trimer formed by NF-YA1, NF-YB1 and NF-YC1 were selected according to their expression pattern in root hairs and tested by coimmunoprecipitation assays",
"The subunits of the trimer formed by NF-YA1, NF-YB7 and NF-YC1 were selected according to their expression pattern at early stages of the symbiotic interaction and tested by coimmunoprecipitation assays",
"The subunits of the trimer formed by NF-YA1, NF-YB1 and NF-YC1 were selected according to their expression pattern at early stages of the symbiotic interaction and tested by bimolecular fluorescence complementation"
] | 10.1104/pp.15.01144 | Legumes | ENVIRONMENT | 10.1104/pp.15.01144 | 2,015 | 25 | 1 | Plant Physiology | true |
How RNAs produced by Bradyrhizobium japonicum can modulate soybean (Glycine max) genes to promote nodulation? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Glycine max"
] | [
"Small fragments of RNA are produced in Bradyrhizobium japonicum by degradation of tRNAs (tRFs) and transported to soybean cells, where postranscriptionally regulate mRNA targets using ARGONAUTE 1 and the host RNAi machinery. tRFs are positive regulators of nodulation since their mRNA targets repress nodule formation.",
"Small fragments of RNA are produced in Bradyrhizobium japonicum by degradation of mRNAs (tRFs) and transported to soybean cells, where postranscriptionally regulate mRNA targets using ARGONAUTE 2 and the host RNAi machinery. tRFs are positive regulators of nodulation since their mRNA targets repress nodule formation.",
"Small fragments of RNA are produced in Bradyrhizobium japonicum by degradation of rRNAs (tRFs) and transported to soybean cells, where postranscriptionally regulate mRNA targets using ARGONAUTE 4 and the host RNAi machinery. tRFs are negative regulators of nodulation since their mRNA targets promote nodule formation."
] | 10.1126/science.aav8907 | Legumes | ENVIRONMENT | 10.1126/science.aav8907 | 2,019 | 221 | 0 | Science | true |
What is the impact of the presence of an IR inserted near the sunflower HaWRKY6 locus? | GENE REGULATION - PTGS | [
"Helianthus annuus"
] | [
"The presence of an IR inserted near the sunflower HaWRKY6 locus regulates the expression of the HaWRKY6 gene by altering the chromatin structure. The IR is transcribed, and its transcript gives rise to 21-nt siRNAs, which trigger posttranscriptional silencing. This epigenetic mark stabilizes the formation of two alternative chromatin loops: one loop forms in cotyledons, enhancing HaWRKY6 transcription, while an alternative intragenic loop forms in leaves, repressing HaWRKY6 transcription.",
"The presence of an IR inserted near the sunflower HaWRKY6 locus regulates the expression of the HaWRKY6 gene by altering the chromatin structure. The IR is transcribed, and its transcript gives rise to 24-nt siRNAs, which trigger DNA methylation. This epigenetic mark stabilizes the formation of two alternative chromatin loops: one loop forms in cotyledons, enhancing HaWRKY6 transcription, while an alternative intragenic loop forms in leaves, repressing HaWRKY6 transcription.",
"The presence of an IR inserted near the sunflower HaWRKY6 locus regulates the expression of the HaWRKY6 gene by altering the promoter efficiency. The IR is transcribed, and its transcript gives rise to 24-nt siRNAs, which trigger DNA methylation. This epigenetic mark stabilizes the formation of two alternative chromatin loops: one loop forms in cotyledons, repressing HaWRKY6 transcription, while an alternative intragenic loop forms in leaves, activating HaWRKY6 transcription."
] | https://doi.org/10.1073/pnas.1903131116 | Other Herbaceous Crops, Spices, Fibers & Weeds | GENE REGULATION | 10.1073/pnas.1903131116 | 2,019 | 41 | 1 | Proceedings of the National Academy of Sciences | true |
How can the insertion of transposon-derived inverted repeats (IRs) impact transcription in Arabidopsis thaliana? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"The presence of transposon-derived inverted repeats (IRs), particularly near coding genes can cause chromatin rearrangements. These rearrangements often lead to the formation of short-range chromatin loops, which are associated with either the activation or repression of transcription in neighboring genes.",
"The presence of transposon-derived inverted repeats (IRs), particularly in non-coding regions can cause chromatin rearrangements. These rearrangements often lead to the formation of long-range chromatin loops, which are associated with either the activation or repression of transcription in neighboring genes.",
"The presence of transposon-derived inverted repeats (IRs), anywhere in the genome can cause chromatin rearrangements. These rearrangements often lead to the formation of short-range chromatin loops, which are associated with the activation of transcription in neighboring genes."
] | https://doi.org/10.1016/j.celrep.2023.112029 | Model Organisms | GENE REGULATION | 10.1016/j.celrep.2023.112029 | 2,023 | 12 | 0 | Cell Reports | true |
How do transposon-derived inverted repeats (IRs) impact the adaptation of Arabidopsis thaliana? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"The natural variation in the presence of transposon-derived inverted repeats (IRs) among Arabidopsis thaliana accessions and their correlation with variations in gene expression can explain the differential phenotypes observed among these accessions. Therefore, IRs represent powerful elements in adaptive evolution.",
"The lack of variation in the presence of transposon-derived inverted repeats (IRs) among Arabidopsis thaliana accessions and their correlation with similar gene expression can explain the lack of differential phenotypes observed among these accessions. Therefore, IRs represent powerful elements in adaptive evolution.",
"The natural variation in the presence of transposon-derived inverted repeats (IRs) among Arabidopsis thaliana accessions and their lack of correlation with variations in gene expression cannot explain the differential phenotypes observed among these accessions. Therefore, IRs do not represent significant elements in adaptive evolution."
] | https://doi.org/10.1016/j.celrep.2023.112029 | Model Organisms | GENE REGULATION | 10.1016/j.celrep.2023.112029 | 2,023 | 12 | 0 | Cell Reports | true |
Is RdDM-dependent silencing of transposable elements always associated with the transcriptional repression of the TEs and their surrounding regions in Arabidopsis? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"In the case of transposon-derived inverted repeats (IRs), non-canonical RdDM, triggered by the production of 24-nt siRNAs from the single-stranded secondary structure formed by Pol IV-driven IR transcription, and the resulting DNA condensation, appears to function differently. For example, it can alter chromatin topology, always increasing transcription of neighboring genes.",
"In the case of transposon-derived inverted repeats (IRs), non-canonical RdDM, triggered by the production of 24-nt siRNAs from the double-stranded secondary structure formed by Pol II-driven IR transcription, and the resulting DNA methylation, appears to function differently. For example, it can alter chromatin topology, either increasing or decreasing transcription of neighboring genes.",
"In the case of transposon-derived inverted repeats (IRs), canonical RdDM, triggered by the production of 21-nt siRNAs from the double-stranded secondary structure formed by Pol II-driven IR transcription, and the resulting DNA methylation, appears to function conservatively. For example, it can alter chromatin condensation causing IR silencing."
] | https://doi.org/10.1016/j.celrep.2023.112029 | Model Organisms | GENE REGULATION | 10.1016/j.celrep.2023.112029 | 2,023 | 12 | 1 | Cell Reports | true |
Which transposable elements have been identified as capable of regulating the expression of the EFR gene in Arabidopsis thaliana? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"A transposon-derived inverted repeat (IR) element located downstream of the EFR gene in Arabidopsis thaliana, named Ea-IR, has the capacity to regulate EFR gene expression. Depending on its methylation state, the Ea-IR can rearrange chromatin topology, creating a short-range chromatin loop that enhance EFR gene expression, ultimately affecting pathogen responses.",
"A transposon-derived inverted repeat (IR) element located upstream of the EFR gene in Arabidopsis thaliana, named Ea-IR, has the capacity to regulate EFR gene expression. Depending on its methylation state, the Ea-IR can rearrange chromatin topology, creating a short-range chromatin loop that inhibiting EFR gene expression, ultimately affecting pathogen responses.",
"A transposon-derived inverted repeat (IR) element located in the second exon of the EFR gene in Arabidopsis thaliana, named Ea-IR, has the capacity to regulate EFR gene expression. Depending on its orientation, the Ea-IR can rearrange itself, enhancing EFR gene expression, ultimately affecting pathogen responses."
] | https://doi.org/10.1101/2023.10.06.561201 | Model Organisms | GENE REGULATION | 10.1101/2023.10.06.561201 | 2,023 | 0 | 0 | null | true |
What are the two main molecular mechanisms for the co-regulation of hypocotyl growth by auxin and gibberellin (GA) in Arabidopsis? | HORMONES | [
"Arabidopsis thaliana"
] | [
"The two primary mechanisms are: (1) Auxin-induced gibberellin catabolism: Auxin stimulates the ARF-dependent transcriptional upregulation of genes encoding GA 2-oxidases, which are key enzymes in gibberellin inactivation. This leads to decreased local GA production in hypocotyl tissues, driving cell elongation. (2) DELLA protein interaction with ARF transcription factors: ARF transcription factors repress cell elongation but are suppressed by their interaction with DELLA proteins. Gibberellins counteract this inhibition by promoting the degradation of DELLA proteins, thereby freeing ARF transcription factors to repress elongation-related processes.",
"The two primary mechanisms are: (1) Auxin-induced gibberellin biosynthesis: Auxin stimulates the ARF-dependent transcriptional upregulation of genes encoding GA 20-oxidases and GA 3-oxidases, which are key enzymes in gibberellin biosynthesis. This leads to increased local GA production in hypocotyl tissues, repressing cell elongation. (2) DELLA protein interaction with ARF transcription factors: ARF transcription factors facilitate cell elongation and are enhanced by their interaction with DELLA proteins. Gibberellins counteract this stimulation by promoting the degradation of DELLA proteins, thereby impairing the promotion by ARF transcription factors of elongation-related processes.",
"The two primary mechanisms are: (1) Auxin-induced gibberellin biosynthesis: Auxin stimulates the ARF-dependent transcriptional upregulation of genes encoding GA 20-oxidases and GA 3-oxidases, which are key enzymes in gibberellin biosynthesis. This leads to increased local GA production in hypocotyl tissues, driving cell elongation. (2) DELLA protein interaction with ARF transcription factors: ARF transcription factors facilitate cell elongation but are suppressed by their interaction with DELLA proteins. Gibberellins counteract this inhibition by promoting the degradation of DELLA proteins, thereby freeing ARF transcription factors to activate elongation-related processes."
] | https://doi.org/10.1104/pp.106.084871 https://doi.org/10.7554/eLife.03031 | Model Organisms | HORMONES | 10.7554/eLife.03031 | 2,014 | 459 | 2 | eLife | true |
What three molecular changes explain the conversion of an ancestral carboxylesterase into a gibberellin receptor? | HORMONES | [
"non-specific"
] | [
"The conversion of an ancestral carboxylesterase into a gibberellin (GA) receptor is explained by the following three molecular changes: (1) Loss of enzymatic activity: The carboxylesterase's enzymatic function was reduced or eliminated, permitting the protein to specialize as a receptor. This loss enabled the focus on gibberellin recognition without interference from the original carboxylesterase activity. (2) Loss of the ligand binding capacity: The ancestral carboxylesterase lost a specific pocket or binding site capable of recognizing gibberellin molecules. (3) Signal transduction adaptation: the ancestral protein developed the ability to phosphorylate DELLA proteins through a newly developed protein kinase domain.",
"The conversion of an ancestral carboxylesterase into a gibberellin (GA) receptor is explained by the following three molecular changes: (1) Gain of enzymatic activity: The carboxylesterase's enzymatic function was enhanced, permitting the protein to specialize as a receptor. This loss enabled the focus on gibberellin recognition in addition to maintaining the original carboxylesterase activity. (2) Structural modification for ligand binding: The ancestral carboxylesterase acquired a specific pocket or binding site capable of recognizing gibberellin molecules. (3) Signal transduction adaptation: the ancestral protein developed the ability to interact with the F-box protein SLEEPY/GID2 through a dedicated surface region.",
"The conversion of an ancestral carboxylesterase into a gibberellin (GA) receptor is explained by the following three molecular changes: (1) Loss of enzymatic activity: The carboxylesterase's enzymatic function was reduced or eliminated, permitting the protein to specialize as a receptor. This loss enabled the focus on gibberellin recognition without interference from the original carboxylesterase activity. (2) Structural modification for ligand binding: The ancestral carboxylesterase acquired a specific pocket or binding site capable of recognizing gibberellin molecules. (3) Signal transduction adaptation: the ancestral protein developed the ability to interact with DELLA proteins through a dedicated surface region."
] | DOI: 10.1073/pnas.1806040115 | Non-specific | HORMONES | 10.1073/pnas.1806040115 | 2,018 | 56 | 2 | Proceedings of the National Academy of Sciences | true |
What is the impact of gibberellins in the control of flowering time in Arabidopsis and what are the main flowering-time genes involved? | HORMONES | [
"Arabidopsis thaliana"
] | [
"Gibberellins are essential to repress flowering under non-inductive short-day conditions. They do it by decreasing the expression of key flowering-time genes, such as LEAFY and SUPPRESSOR OF CONSTANS OVEREXPRESSION (SOC1). ",
"Gibberellins are essential to promote flowering under non-inductive short-day conditions. They do it by enhancing the expression of key flowering-time genes, such as LEAFY and SUPPRESSOR OF CONSTANS OVEREXPRESSION (SOC1). ",
"Gibberellins are essential to promote flowering under long day conditions. They do it by enhancing the expression of key flowering-time genes, such as FLOWERING LOCUS C (FLC) and SUPPRESSOR OF CONSTANS OVEREXPRESSION (SOC1). "
] | DOI: 10.1105/tpc.10.5.791. doi: 10.1046/j.1365-313x.2003.01833.x | Model Organisms | HORMONES | 10.1046/j.1365-313x.2003.01833.x | 2,003 | 463 | 1 | The Plant Journal | true |
What molecular mechanisms regulate DELLA activity in Arabidopsis, beyond the control of cellular DELLA levels? | HORMONES | [
"Arabidopsis thaliana"
] | [
"DELLA activity, defined by the interaction with transcription factors and other transcriptional regulators, is regulated by postranslational modifications that alter DELLA’s capacity to establish these interactions. Among them, three are the best studied ones: In Arabidopsis, O-fucosylation catalyzed by SPINDLY (SPY) stimulates the interaction with PIF transcription factors, while O-GlcNAcylation catalyzed by SECRET AGENT (SEC) impairs this interaction. Finally, SUMOylation has been described in rice to differentially affect the interaction with distinct transcription factors, leading to salt stress tolerance.",
"DELLA activity, defined by the interaction with transcription factors and other transcriptional regulators, is regulated by postranslational modifications that alter DELLA’s capacity to establish these interactions. Among them, three are the best studied ones: In Arabidopsis, O-fucosylation catalyzed by SECRET AGENT (SEC) impairs the interaction with PIF transcription factors, while O-GlcNAcylation catalyzed by SPINDLY (SPY) promotes this interaction. Finally, SUMOylation has been described in rice to differentially affect the interaction with distinct transcription factors, leading to salt stress tolerance.",
"DELLA activity, defined by the interaction with transcription factors and other transcriptional regulators, is regulated by postranslational modifications that alter DELLA’s capacity to establish these interactions. Among them, three are the best studied ones: In Arabidopsis, O-fucosylation catalyzed by SPINDLY (SPY) represses the interaction with PIF transcription factors, while O-GlcNAcylation catalyzed by SECRET AGENT (SEC) stimulates this interaction. Finally, phosphorylation has been described in rice to differentially affect the interaction with distinct transcription factors, leading to salt stress sensitivity."
] | doi: 10.1101/gad.270587.115. doi: 10.1038/nchembio.2320. doi: 10.1007/s00425-024-04565-1 | Model Organisms | HORMONES | 10.1007/s00425-024-04565-1 | 2,024 | 0 | 0 | Planta | true |
What is the experimental evidence for the involvement of NPF3 in gibberellin-dependent regulation of Arabidopsis root growth? | HORMONES | [
"Arabidopsis thaliana"
] | [
"NPF3 is a gibberellin influx carrier expressed in the root endodermis. Gibberellin accumulation in the endodermis drives cell expansion in this cell type, from which growth of the whole organ is coordinated. Overexpression of NPF3 causes a phenotype associated to gibberellin hypersensitivity in roots.",
"NPF3 is a gibberellin influx carrier expressed everywhere in the root except in the endodermis. Gibberellin deprivation in the root endodermis promotes cell expansion in this cell type, from which growth of the whole organ is coordinated. Overexpression of NPF3 causes a phenotype associated to gibberellin deficiency in roots.",
"NPF3 is a gibberellin efflux carrier expressed in the root endodermis. Gibberellin accumulation in the endodermis prevents cell expansion in this cell type, from which growth of the whole organ is coordinated. Overexpression of NPF3 causes a phenotype associated to gibberellin deficiency in roots."
] | doi: 10.1038/ncomms11486 | Model Organisms | HORMONES | 10.1038/ncomms11486 | 2,016 | 181 | 0 | Nature Communications | true |
Does the alfalfa dwarf cytorebdovirus P protein exhibit activity as a suppressor of local and/or systemic RNA silencing? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
" The phosphoprotein (P) encoded by alfalfa dwarf virus (ADV) is a suppressor of RNA silencing. ADV P has a very strong local suppressor activity and prevents RNAi accumulation, but weakly suppresses systemic RNA silencing. Protein-protein interaction assays determined that the suppression mechanism appears to involve the binding of ADV P to the RNA-induced silencing complex protein AGO2 and probably works by inhibiting miRNA-guided AGO2 cleavage and prevents transitive amplification by repressing secondary RNAi production.",
"The phosphoprotein (P) encoded by alfalfa dwarf virus (ADV) is not a suppressor of RNA silencing. P from ADV has no local or systemic suppressor activity on RNA silencing. Protein-protein interaction assays have shown that it does not present a suppression mechanism since it does not bind to any of the secondary RNA silencing complex proteins.",
" The phosphoprotein (P) encoded by alfalfa dwarf virus (ADV) is a suppressor of RNA silencing. ADV P has relatively weak local suppressor activity but strongly suppresses systemic RNA silencing. Protein-protein interaction assays determined that the suppression mechanism appears to involve binding of ADV P to the RNA-induced silencing complex proteins AGO1 and AGO4. ADV P likely functions by inhibiting miRNA-guided cleavage of AGO1 and prevents transitive amplification by repressing secondary siRNA production."
] | http://dx.doi.org/10.1016/j.virusres.2016.08.008 | Non-specific | ENVIRONMENT | 10.1016/j.virusres.2016.08.008 | 2,016 | 16 | 2 | Virus Research | true |
Is the transmission of CMV through seeds possible in pepper, and if so, what is the estimated rate of such transmission? | ENVIRONMENT - BIOTIC STRESS | [
"Capsicum annuum"
] | [
" When CMV seed growth tests were performed in pepper pots, no transmission was detected in either the seed coat or the embryo. The final transmission rate of the seeds was 0%.",
" When CMV seed growth tests were performed in pots on peppers, transmission was detected only in seed coat. CMV infection in seeds ranged from 10 to 15% for the coat. While the final transmission rate from seeds was approximately 82 to 84%.",
"When CMV seed growth tests were performed in pots on peppers, transmission was detected in both the seed coat and the embryo. CMV infection in seeds ranged from 53 to 83% for the coat and from 10 to 46% for the embryo. While the final transmission rate from seeds was approximately 10 to 14%."
] | doi:10.1016/j.jviromet.2009.09.026 | Solanaceae & Relatives | ENVIRONMENT | 10.1016/j.jviromet.2009.09.026 | 2,010 | 60 | 2 | Journal of Virological Methods | true |
What is the relationship between the efficiency of PVY inhibition across multiple strains (PVYN, PVYO, and PVYNTN) and the expression of Cas13 with specific gRNA cassettes in transgenic potato lines? | ENVIRONMENT - BIOTIC STRESS | [
"Solanum tuberosum"
] | [
"Efficiency of PVY inhibition against multiple strains of PVYN, PVYO, and PVYNTN does not correlate with Cas13 with specific gRNA cassette expression in transgenic potato lines.",
" Efficiency of PVY inhibition against multiple strains of PVYN, PVYO, and PVYNTN positively correlated with Cas13 with specific gRNA cassette expression in transgenic potato lines.",
"Efficiency of PVY inhibition against multiple strains of PVYN, PVYO, and PVYNTN negatively correlated with Cas13 with specific gRNA cassette expression in transgenic potato lines."
] | https://doi.org/10.1080/21645698.2022.2080481 | Solanaceae & Relatives | ENVIRONMENT | 10.1080/21645698.2022.2080481 | 2,022 | 13 | 1 | GM Crops & Food | true |
What is the effect of silencing the stress-induced gene encoding Kunitz peptidase inhibitor-like protein on the death rate of TMV-infected Nicotiana benthamiana plants ? | ENVIRONMENT - BIOTIC STRESS | [
"Nicotiana benthamiana"
] | [
"Compared to both the control group and plants with elevated KPILP levels in Nicotiana benthamiana, silencing the stress-induced gene encoding Kunitz peptidase inhibitor-like protein (KPILP) increases the death rate of TMV-infected plants. Systemic infection of N. benthamiana plants with tobacco mosaic virus (TMV) induces a reduction in KPILP mRNA accumulation. KPILP knockdown significantly reduces the efficiency of TMV and or the closely related crucifer-infecting tobamovirus (crTMV) intercellular transport but not in the reproduction rate.",
"Compared to both the control group and plants with elevated KPILP levels in Nicotiana benthamiana, silencing the stress-induced gene encoding Kunitz peptidase inhibitor-like protein (KPILP) reduces the death rate of TMV-infected plants. Systemic infection of N. benthamiana plants with tobacco mosaic virus (TMV) induces a drastic increase in KPILP mRNA accumulation. KPILP knockdown significantly reduces the efficiency of TMV and or the closely related crucifer-infecting tobamovirus (crTMV) intercellular transport and reproduction",
"Compared with the control group and plants with elevated levels of KPILP in Nicotiana benthamiana, stress-induced silencing of the gene encoding Kunitz inhibitor peptidase-like protein (KPILP) does not produce any change in the death rate of TMV-infected plants. KPILP mRNA accumulation does not change by an systemic infection of N. benthamiana plants with tobacco mosaic virus (TMV). KPILP knockdown significantly reduces the efficiency of TMV intercellular transport and reproduction but do not alter the ffeciency of the closely related crucifer-infecting tobamovirus (crTMV)."
] | https://doi.org/10.3389/fpls.2023.1224958 | Solanaceae & Relatives | ENVIRONMENT | 10.3389/fpls.2023.1224958 | 2,023 | 5 | 1 | Frontiers in Plant Science | true |
Considering emerging studies, what are the critical factors contributing to the manifestation of virus-induced symptoms in plants through the manipulation of plant cellular processes by viruses? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
" Key factors involved in the mechanisms by which viruses manipulate plant cellular processes inducing symptoms have been identified as hormonal manipulation and gene expression changes.",
"Key factors involved in the mechanisms by which viruses manipulate plant cellular processes inducing symptoms have been identified as chloroplast protein dysfunction, and hormonal manipulation, metabolic disorder.",
"Key factors involved in the mechanisms by which viruses manipulate plant cellular processes inducing symptoms have been identified as chloroplast protein dysfunction, hormonal manipulation, ROS accumulation and cell cycle control."
] | https://doi.org/10.3390/plants12152830 | Non-specific | ENVIRONMENT | 10.3390/plants12152830 | 2,023 | 26 | 2 | Plants | true |
Which gene was targeted using CRISPR/Cas9 to delay flowering time in Medicago sativa (alfalfa)? | PLANT BIOTECHNOLOGY | [
"Medicago sativa"
] | [
"The polyester synthase-like gene At1g73750 has been disrupted using CRISPR/Cas9 to delay flowering time in Medicago sativa.",
"The FT1 gene has been disrupted using CRISPR/Cas9 to delay flowering time in Medicago sativa.",
"The polyester synthase-like gene MSAD_264347 has been disrupted using CRISPR/Cas9 to delay flowering time in Medicago sativa."
] | https://doi.org/10.1007/s00299-023-02997-9 | Legumes | PLANT BIOTECHNOLOGY | 10.1007/s00299-023-02997-9 | 2,023 | 2 | 2 | Plant Cell Reports | true |
What is one of the main challenges in applying CRISPR/Cas9 technology to crop genomes? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Efficient delivery of CRISPR/Cas9 components into plant cells and successful regeneration of edited plants.",
"CRISPR/Cas9 cannot target coding regions of plant genomes due to polyploidy.",
"CRISPR/Cas9 requires the presence of specific RNA polymerases unique to animals, making it less efficient in plants."
] | https://doi.org/10.1016/j.plantsci.2023.111809 | Non-specific | PLANT BIOTECHNOLOGY | 10.1016/j.plantsci.2023.111809 | 2,023 | 0 | 0 | Plant Science | true |
How does the Protospacer Adjacent Motif (PAM) influence the CRISPR/Cas9 genome editing process? | GENOME AND GENOMICS | [
"non-specific"
] | [
"The PAM sequence determines the efficiency of DNA repair after Cas9 introduces a double-strand break.",
"The PAM sequence is incorporated into the guide RNA to enhance its stability during the editing process.",
"The PAM sequence is required for Cas9 to identify and bind the target DNA site, enabling precise cleavage."
] | https://doi.org/10.1093/aob/mcae191 | Non-specific | GENOME AND GENOMICS | 10.1093/aob/mcae191 | 2,024 | 0 | 2 | Annals of Botany | true |
What is the impact of disrupting the SPL13 gene in lettuce via genome editing, and why could this strategy be useful for developing a commercial variety? | PLANT BIOTECHNOLOGY | [
"Lactuca sativa"
] | [
"Disrupting the SPL13 gene in lettuce via genome editing delays flowering, increases biomass, and enhances leaf production. This strategy is useful for developing a commercial variety as it extends the vegetative growth phase, resulting in higher yields and improved agronomic traits that are desirable for market production.",
"Disrupting the SPL13 gene in lettuce via genome editing accelerates flowering, decreases biomass, and reduces leaf production. This strategy is not ideal for developing a commercial variety as it shortens the vegetative phase, limiting yield potential and agronomic value.",
"Disrupting the SPL13 gene in lettuce via genome editing enhances drought tolerance, increases water-use efficiency, and improves photosynthesis rates. This strategy is useful for developing a commercial variety in water-scarce environments but does not directly affect flowering time or biomass production."
] | https://doi.org/10.1007/s00299-022-02952-0 | Other Herbaceous Crops, Spices, Fibers & Weeds | PLANT BIOTECHNOLOGY | 10.1007/s00299-022-02952-0 | 2,022 | 6 | 0 | Plant Cell Reports | true |
Which genes were successfully modified using cytosine base editing (CBE) in alfalfa to confer herbicide tolerance, and why was a dead Cas9 (dCas9) used in this process? | PLANT BIOTECHNOLOGY | [
"Medicago sativa"
] | [
"The ALSI and ALSII genes were successfully modified using CBE to confer herbicide tolerance. A dead Cas9 (dCas9), fused to a cytosine deaminase, was used to cleave the DNA at specific sites, enabling the integration of a resistance gene into the target locus.",
"The ALS1 and ALS2 genes were successfully modified using CBE to confer herbicide tolerance. A dead Cas9 (dCas9), fused to a cytosine deaminase, was used to facilitate precise base substitutions without creating double-strand breaks, generating a new allele with a single nucleotide change.",
"The ALSI and ALSII genes were successfully modified using CBE to confer herbicide tolerance. A dead Cas9 (dCas9), fused to a cytosine deaminase, was used to alter the target site by introducing insertions and deletions that disrupt gene function."
] | https://doi.org/10.1007/s00299-021-02827-w | Legumes | PLANT BIOTECHNOLOGY | 10.1007/s00299-021-02827-w | 2,022 | 15 | 1 | Plant Cell Reports | true |
Which is the master regulator gene involved in branching regulation in Arabidopsis thaliana? And how is it expression regulated? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, the master regulator of branching is BRANCHED1 (BRC1), a transcription factor from the TCP class II family. This gene is regulated by numerous environmental and endogenous conditions. Regarding environmental conditions, being shaded by neighbor plants or increasing far red light promote BRC1 expression. As to endogenous conditions, there is a regulation mediated by hormones. Cytokinins down regulate BRC1 while strigolactones increase its transcription levels. Also sucrose down regulates BRC1 expression. ",
"The master regulator gene of branching in Arabidopsis thaliana is FLC, a MADS-domains transcription factor. This gene is repressed after a prolonged period of low temperatures. Also FRIGIDA (FRI) increases the FLC protein production, while VERNALIZATION INSENSITIVE3 (VIN3) reduces FLC transcriptional activity during vernalization. ",
"BRANCHED1 is the master regulator of branching in Arabidopsis. This gene promotes axillary bud outgrowth integrating different signals as cold or blue light. Also its transcription level increase with high levels of sucrose."
] | doi: 10.3389/fpls.2014.00741 | Model Organisms | GROWTH AND DEVELOPMENT | 10.3389/fpls.2014.00741 | 2,015 | 222 | 0 | Frontiers in Plant Science | true |
How is the long noncoding RNA APOLO involved in the regulation of branching in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The long non coding RNA APOLO participates in branching regulation through the epigenetic modulation of BRC1expression. This regulation occurs in the context of shade or under high levels of far red light. Different levels of APOLO modulate a chromatin loop opening or formation. This chromatin loop encompasses BRC1 and its neighbor gene’s promoters so, when it is open it allows the transcription of both genes but, when it is formed, the transcription levels of both decrease. ",
"The long non coding RNA APOLO participates in branching regulation by increasing strigolactones levels. ",
"The long non coding RNA APOLO participates in branching regulation by modulating FLC expression. This regulation occurs in the context of low temperatures. "
] | DOI 10.15252/embj.2023113941 | Model Organisms | GROWTH AND DEVELOPMENT | 10.15252/embj.2023113941 | 2,023 | 3 | 0 | The EMBO Journal | true |
In which context does the long noncoding RNA APOLO participate in BRC1 expression modulation in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The long non coding RNA APOLO modulates BRC1 expression in the context of shade or under high far red light levels.",
"The long non coding RNA APOLO modulates BRC1 expression in the context of low far red levels.",
"The long non coding RNA APOLO modulates BRC1 expression in the context of high temperatures"
] | DOI 10.15252/embj.2023113941 | Model Organisms | GROWTH AND DEVELOPMENT | 10.15252/embj.2023113941 | 2,023 | 3 | 0 | The EMBO Journal | true |
Which are the most important responses of Arabidopsis thaliana plants to the shade avoidance syndrome? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, shade light signals delay flowering and promote branching. ",
"In Arabidopsis thaliana, the shade avoidance syndrome induces seeds germination and suppresses hypocotyl and petiole elongation.",
"In Arabidopsis thaliana, the shade avoidance syndrome presents different responses depending on the plant developmental stage. In seeds, shade light signals repress germination. At seedling stage, promote hypocotyl elongation. At the rosette stage, promote petiole elongation, reduce leaf lamina expansion and induce hyponasty. Also, accelerate flowering and reduce branching. "
] | doi: 10.1199/tab.0157 | Model Organisms | ENVIRONMENT | 10.1199/tab.0157 | 2,012 | 311 | 2 | The Arabidopsis Book | true |
How is hyponasty regulated in Arabidopsis thaliana? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"The hyponasty response is the leaf upward movement driven by a higher rate of cell expansion on de abaxial side compared with the adaxial. This difference in cell expansion depends on auxin biosynthesis, transport and distribution, which is regulated by R/FR light. Low R/FR inactivates phyB, allowing PIFs to accumulate and become active to control transcription of target genes including YUCs which are involved in auxin biosynthesis. Also there are some evidences that the long non coding RNA APOLO has a role in the hyponastic response to a low R/FR through the modulation of some genes. APOLO is induced by auxin, regulates genes involved in auxin biosynthesis like YUC2 and participates in auxin redistribution modulating PID and WAG2 expression. ",
"The hyponasty response is the leaf upward movement driven by a higher rate of cell expansion on de adaxial side compared with the abaxial. This difference in cell expansion depends on gibberellin biosynthesis and distribution, which is regulated by R/FR light. Low R/FR inactivates phyB, allowing PIFs to accumulate and become active to control transcription of target genes including YUCs which are involved in ethylene biosynthesis. ",
"The hyponasty response is regulated by cold temperatures through the long non coding RNA CIL1 action."
] | DOI 10.15252/embj.2023113941 | Model Organisms | ENVIRONMENT | 10.15252/embj.2023113941 | 2,023 | 3 | 0 | The EMBO Journal | true |
Which genes (AGI) encode structural proteins of cytochrome c oxidase in Arabidopsis thaliana? Mention whether there is homology with any yeast and/or mammalian genes? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Cytochrome c Oxidase is composed of several subunits in Arabidopsis thaliana. The enzymatic core is highly conserved between plants, mammals and yeasts and the genes are normally encoded by the mitochondrial genome. The Arabidopsis genes are COX1 (ATMG01360), COX2 (ATMG00160) and COX3 (ATMG01520). The rest of the subunits are encoded in the nuclear genome and only some of them are conserved, including COX10 (AT2G44520), COX11 (AT1G02410), COX15, (AT5G56090), COX17 (AT3G15352 and AT1G53030) and COX19 (AT1G66590 and AT1G52710), and all of them have the same name in mammals and yeast. There are also other genes found in proteomic analysis, but without a clear function, such as COX6b-1 to 4, COX6a whose mammalian counterparts have the same name and are COX12 and Cox13 in yeast. Finally, there are other genes exclusive to plants such as COX5c-1 to 3 and COX-X1 to 6",
"The Arabidosis Cytochrome c Oxidase CcO catalytic core is encoded by 3 mitochondrial gene, COX1 (ATMG00460), COX2 (ATMG00760) and COX2 (ATMG00550), all of them present conserved homologous in mammals and yeast. The rest of the subunits are also encoded in the mitochondrial genome and only some of them are conserved, including COX5b-1 to 3 (ATMG00455, ATMG00410, ATMG01160), homologous to COX5b of mammals and Cox4 of yeast. Also, other proteins are part of the enzyme and act as regulatory modules, among them we can find COX10 (AT2G44520), COX11 (AT1G02410), COX15, (AT5G56090), COX17 (AT3G15352 and AT1G53030) and COX19 (AT1G66590 and AT1G52710), and all of the have the same name in mammals and yeast. ",
"ytochrome c Oxidase is composed of several subunits in Arabidopsis thaliana. The enzymatic core is highly conserved between plants, mammals and yeasts and the genes are normally encoded by the mitochondrial genome. The Arabidopsis genes are COX1 (ATMG01360), COX2 (ATMG00160) and COX3 (ATMG00730). The rest of the subunits are encoded in the nuclear genome and only some of them are conserved, including COX5b-1 to 3 (AT3G15640, AT1G80230, AT1G52710), homologous to COX5b of mammals and Cox4 of yeast. All of these subunits are necessary for the correct assembly and function of the enzyme. There are also other genes found in proteomic analysis, but without a clear function, such as COX6b-1 to 4, COX6a whose mammalian counterparts have the same name and are COX12 and Cox13 in yeast. Finally, there are other genes exclusive to plants such as COX5c-1 to 3 and COX-X1 to 6.\n"
] | https://doi.org/10.3390/ijms19030662 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.3390/ijms19030662 | 2,018 | 97 | 2 | International Journal of Molecular Sciences | true |
Describe the main phenotypes of the Cytochrome c mutants in Arabidopsis thaliana and the associated molecular pathways that are affected | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
" Arabidopsis thaliana has 2 genes that encode for the heme protein Cytochrome c, CYTC-1 and CYTC-2. This protein is involved in the electron transfer between complex III and complex IV of the mitochondrial electron transport chain. The mutation in the CYTC genes in Arabidopsis generates different phenotypes depending on the mutant analyzed. Double knock-out mutants are embryo lethal. The mutants knock-down in CYTC-1 and knock-out in CYTC-2 that have very low levels of CYTC protein present a reduced growth rate and early flowering. These phenotypes are mostly associated with the CYTC-2 gene. The reduced growth rate is associated with a lower level of ATP, which generates a lower activation of the SnRK2-pathway and reduces the autophagy to adjust growth and cellular energy production. On the other hand, the CYTC-1 gene presents redundancy with CYTC-2 in all the phenotypes and this could be explained due to both genes have almost identical protein sequence and very similar expression pattern but the CYT-C2 expression is stronger, masking CYT-C1 mutations effects.\n",
"Arabidopsis thaliana has 2 genes that encode for the heme protein Cytochrome c, CYTC-1 and CYTC-2. This protein is involved in the electron transfer between complex III and complex IV of the mitochondrial electron transport chain. The mutation in the CYTC genes in Arabidopsis generates different phenotypes depending on the mutant analyzed. Double knock-out mutants are embryo lethal. The mutants knock-down in CYTC-1 and knock-out in CYTC-2 that have very low levels of CYTC protein present a reduced growth rate and late flowering. These phenotypes are mostly associated with the CYTC-1 gene. The reduced growth rate is associated with a higher level of NADH, which generates a lower activation of the TOR-pathway and reduces the autophagy to adjust growth and cellular energy production. On the other hand, the CYTC-2 gene presents redundancy with CYTC-1 in most of the phenotypes with the only exception found during the germination process. During germination, CYTC-2 is repressed due to the decrease in ABI4, and it decreases the sensitivity to ABA stimulating the germination.",
"Arabidopsis thaliana has 2 genes that encode for the heme protein Cytochrome c, CYTC-1 and CYTC-2. This protein is involved in the electron transfer between complex III and complex IV of the mitochondrial electron transport chain. The mutation in the CYTC genes in Arabidopsis generates different phenotypes depending on the mutant analyzed. Double knock-out mutants are embryo lethal. The mutants knock-down in CYTC-1 and knock-out in CYTC-2 that have very low levels of CYTC protein present a reduced growth rate and late flowering. These phenotypes are mostly associated with the CYTC-1 gene. The reduced growth rate is associated with a lower synthesis of ATP, which generates a lower activation of the TOR-pathway and an increase in autophagy to adjust growth and cellular energy production. On the other hand, the CYTC-2 gene presents redundancy with CYTC-1 in most of the phenotypes with the only exception found during the germination process. During germination, CYTC-2 is de-repressed due to the decrease in ABI4, stimulating the synthesis of the ATP required for this process, in addition the increase in CYTC-2 decreases the sensitivity to ABA."
] | https://doi.org/10.1111/tpj.13845, https://doi.org/10.1111/nph.18287, https://doi.org/10.1111/nph.19506, | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1111/nph.19506 | 2,024 | 6 | 2 | New Phytologist | true |
Does the Arabidopsis cytochrome CYT-C2 gene have any function that is not redundant with the CYT-C1 gene? If there is any molecular mechanism described, please explain it. | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Both CYT-C genes present redundancy in most biological processes. This is because both are the result of a recent duplication. However, beyond the fact that at the protein sequence level they are practically identical, their promoters have different expression patterns. During germination, a repression of the CYT-C2 gene occurs caused by the decrease in ABA levels and less activation of the transcription factors of the ABI family, particularly ABI4. The decrease in CYT-C2 reduces the synthesis of ATP at the mitochondrial level increasing the Reactive oxygen species that are crucial in this process. In addition, this decrease in CYT-C2 reduces the sensitivity to ABA in seeds, stimulating germination.",
"Both CYT-C genes present redundancy in most biological processes. This is because both are the result of a recent duplication. However, beyond the fact that at the protein sequence level they are practically identical, their promoters have different expression patterns. During germination, a de-repression of the CYT-C2 gene occurs caused by the decrease in ABA levels and less activation of the transcription repressor factors of the ABI family, particularly ABI4, which bind the G-BOX sites present in the CYT-C2 promoter. The increase in CYT-C2 during germination stimulates the synthesis of ATP at the mitochondrial level, which is essential for this process. Furthermore, this increase in CYT-C2 decreases the sensitivity to ABA in seeds, stimulating germination",
"Both CYT-C genes present redundancy in most biological processes. This is because both are the result of a recent duplication. However, beyond the fact that at the protein sequence level they are practically identical, their promoters have different expression patterns. During germination, a de-repression of the CYT-C2 gene occurs caused by the decrease in ABA levels and less activation of the transcription repressor factors of the HD-zip family, particularly HB40, which bind the G-BOX sites present in the CYT-C2 promoter. The increase in CYT-C2 during germination stimulates the synthesis of ATP at the mitochondrial level, which is essential for this process. Furthermore, this rise in CYT-C2 increase the gibberellin synthesis in seeds, stimulating germination."
] | https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18287 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1111/nph.18287 | 2,022 | 9 | 1 | New Phytologist | true |
In the aerial tissue of plant organisms, both chloroplasts and mitochondria have the capacity to synthesize ATP. In Arabidopsis, do cytoplasmic and nuclear metabolism directly use ATP from both sources equally? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Currently, very few studies have delved into this topic. However, the use of fluorescent ATP sensors has allowed the evaluation of the level of ATP in the cytoplasm of different Arabidopsis tissues, under light and dark conditions. In addition, the evolution of ATP was evaluated by inhibiting the mitochondrial electron transport chain with antimycin A. According to what was reported by this sensor, in light condition, the level of cytoplasmic ATP drops around 60% when mitochondrial production is blocked. The same does not happen when the measurement is made in darkness where chloroplast ATP synthesis is stopped. Due to this, the authors of this work conclude that probably around half of the ATP used in cytoplasmic metabolism is generated in the mitochondria, in light. In darkness the ATP is provided almost exclusively by the mitochondria.",
"Currently, very few studies have delved into this topic. However, the use of fluorescent ATP sensors has allowed the evaluation of the level of ATP in the cytoplasm of different Arabidopsis tissues, under light and dark conditions. In addition, the evolution of ATP was evaluated by inhibiting the mitochondrial electron transport chain with antimycin A. According to what was reported by this sensor, the level of cytoplasmic ATP drops abruptly when mitochondrial production is blocked in darkness. The same does not happen when the measurement is made in light where chloroplast ATP synthesis is active. Due to this, the authors of this work conclude that probably most of the ATP used in cytoplasmic metabolism is generated in chloroplast under light conditions, and by the mitochondria in darkness.",
"Currently, very few studies have delved into this topic. However, the use of fluorescent ATP sensors has allowed the evaluation of the level of ATP in the cytoplasm of different Arabidopsis tissues, under light and dark conditions. In addition, the evolution of ATP was evaluated by inhibiting the mitochondrial electron transport chain with antimycin A. According to what was reported by this sensor, the level of cytoplasmic ATP drops abruptly when mitochondrial production is blocked. The same does not happen when the measurement is made in darkness where chloroplast ATP synthesis is stopped. Due to this, the authors of this work conclude that probably most of the ATP used in cytoplasmic metabolism is generated in the mitochondria, both in light and in darkness.\n"
] | https://doi.org/10.7554/eLife.26770 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.7554/eLife.26770 | 2,017 | 130 | 2 | eLife | true |
The COX10 and COX15 genes are involved in the biosynthesis of the heme a group, which is essential for the assembly of cytochrome c oxidase (CcO) in humans and yeasts. Are there homologs of these genes in Arabidopsis? Is their function conserved? Is there a molecular mechanism that describes its participation in the biosynthesis of the heme a and assembly of CcO in Arabidopsis? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Both genes have homologs encoded in the Arabidopsis genome. COX10 is encoded in the locus AT2G44520, while COX15 is encoded in AT5G56090. The function of both genes in the assembly of CcO would be conserved, since these Arabidopsis thaliana genes are able to rescue mitochondrial respiration in mutants of its homologs in Saccharomyces cerevisiae. Furthermore, the Arabidopsis null mutant of both genes are embryo lethal, displaying very low histochemical CcO activity staining. Heterozygous COX10 mutant plants show reduced respiration rates in leaves and seeds, probably caused by a decrease in assembled and functional CcO. A similar observation was made in a heterozygous mutant of COX15. These observations are similar to those found in yeast or mammals, and it is attributed to the fact that both proteins catalyze consecutive biochemical steps and both are necessary for the heme a biosynthesis. In line with this, these plants accumulate the precursor heme b and have lower levels of heme o and a.",
" Both genes have homologs encoded in the Arabidopsis genome. COX10 is encoded in the locus AT1G24720, while COX15 is encoded in AT2G43090. The function of the COX10 gene in the assembly of CcO would be conserved, since this Arabidopsis thaliana gene is able to rescue mitochondrial respiration in mutants of its homolog in Saccharomyces cerevisiae. Furthermore, Heterozygous mutant plants show reduced respiration rates in leaves and seeds, probably caused by a decrease in assembled and functional CcO. Also these plants accumulate the precursor heme b and have lower levels of heme o and a. This is explained because it is not converted by the absence of COX10. On the other hand, there are no studies on the function of the Arabidopsis COX15 gene.",
"Both genes have homologs encoded in the Arabidopsis genome. COX10 is encoded in the locus AT2G44520, while COX15 is encoded in AT5G56090. The function of the COX10 gene in the assembly of CcO might be conserved, since this Arabidopsis thaliana gene is able to rescue mitochondrial respiration in mutants of its homolog in Saccharomyces cerevisiae. Furthermore, the Arabidopsis null mutant is embryo lethal, displaying very low histochemical CcO activity staining. Heterozygous mutant plants show reduced respiration rates in leaves and seeds, probably caused by a decrease in assembled and functional CcO. However, there is no direct evidence associating this protein with heme a biosynthesis in Arabidopsis. On the other hand, there are no studies on the function of the Arabidopsis COX15 gene."
] | https://doi.org/10.1093/jxb/erv381, https://doi.org/10.3390/ijms19030662 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.3390/ijms19030662 | 2,018 | 97 | 2 | International Journal of Molecular Sciences | true |
How LncRNA MSTRG.13420 formed R-loop functions in cold response of rice? | GENOME AND GENOMICS | [
"Oryza sativa"
] | [
"LncRNA MSTRG.13420 located in downstream region of OsDof16 was transcribed from antisense strand and significantly downregulated in cold treatment. LncRNA MSTRG.13420 formed R-loop to negatively regulate OsDof16, and act as posstive regulator in cold response in rice.",
"LncRNA MSTRG.13420 located in promoter of OsDof16 was transcribed from antisense strand and significantly downregulated in cold treatment. LncRNA MSTRG.13420 formed R-loop to positively regulate OsDof16, and act as negative regulator in cold response in rice.",
"LncRNA MSTRG.13420 located in promoter of OsDof16 was transcribed from sense strand and significantly upregulated in cold treatment. LncRNA MSTRG.13420 formed R-loop to negatively regulate OsDof16, and act as posstive regulator in cold response in rice."
] | 10.1111/nph.19315. | Model Organisms | GENOME AND GENOMICS | 10.1111/nph.19315 | 2,023 | 2 | 1 | New Phytologist | true |
What’s the relationship between DNA G4 intensity and expression levels of G4-overlapping genes in rice genome? | GENOME AND GENOMICS | [
"Oryza sativa"
] | [
"G4s intensity exhibited a negative association with expression levels of G4-overlapping genes at transcript end sites (TTSs), while G4s in gene bodies was positively corresponded with expression levels.",
"G4s intensity exhibited a positive association with expression levels of G4-overlapping genes at transcript start sites (TSSs), while G4s at transcript end sites (TTSs) was negatively corresponded with expression levels.",
"G4s intensity exhibited a positive association with expression levels of G4-overlapping genes at transcript start sites (TSSs), while G4s in gene bodies was negatively corresponded with expression levels."
] | doi: 10.1093/plphys/kiab566. | Model Organisms | GENOME AND GENOMICS | 10.1093/plphys/kiab566 | 2,021 | 28 | 2 | Plant Physiology | true |
How 5mC DNA methylation affect i-motif formation under different pH condition in rice genome? | GENOME AND GENOMICS | [
"Oryza sativa"
] | [
"Subset of i-motif folded at pH 5.5 show high methylation levels than those folded at pH 7.0, and core regions of i-motifs trend to be higher methylated than flank regions.",
"Subset of i-motif folded at pH 7.0 show high methylation levels than those folded at pH 5.5, and flank regions of i-motifs trend to be higher methylated than core regions.",
"Subset of i-motif folded at pH 7.0 show high methylation levels than those folded at pH 5.5, and core regions of i-motifs trend to be higher methylated than flank regions."
] | 10.1093/nar/gkad1245. | Model Organisms | GENOME AND GENOMICS | 10.1093/nar/gkad1245 | 2,024 | 8 | 2 | Nucleic Acids Research | true |
In which genomic regions the i-motif structure trend to be present or depleted? | GENOME AND GENOMICS | [
"Oryza sativa"
] | [
"The rice genome was divided into seven genomic subregions, including 5′UTRs, 3′UTRs, exons, introns, downstream and distal intergenic regions. The i-motif structure trend to present in promoters and 5′UTRs, and depleted in exons and distal intergenic regions.",
"The rice genome was divided into seven genomic subregions, including 5′UTRs, 3′UTRs, exons, introns, downstream and distal intergenic regions. The i-motif structure trend to present in downstream and 3′UTRs, and depleted in exons and introns regions.",
"The rice genome was divided into seven genomic subregions, including 5′UTRs, 3′UTRs, exons, introns, downstream and distal intergenic regions. The i-motif structure trend to present in exons and 5′UTRs, and depleted in introns and distal intergenic regions."
] | 10.1093/nar/gkac121. | Model Organisms | GENOME AND GENOMICS | 10.1093/nar/gkac121 | 2,022 | 34 | 0 | Nucleic Acids Research | true |
What are the intrinsic sequence feature for Cold-induced R-loop regions. | GENOME AND GENOMICS | [
"Oryza sativa"
] | [
"Cold-induced R-loops have highest GC content compare to other genomic regions, GCGGC and CCTCC binding motifs of C2H2 family were enriched in Cold-induced R-loops, which were reported to be involved in plant stress response.",
"Cold-induced R-loops have highest GC content compare to other genomic regions, CCGCC and CCTCC binding motifs of AP2-EREBP family were enriched in Cold-induced R-loops, which were reported to be involved in plant stress response.",
"Cold-induced R-loops have lowest GC content compare to other genomic regions, CGCC and CCTCC binding motifs of AP2-EREBP family were enriched in Cold-induced R-loops, which were reported to be involved in rice root development ."
] | 10.1111/nph.19315. | Model Organisms | GENOME AND GENOMICS | 10.1111/nph.19315 | 2,023 | 2 | 1 | New Phytologist | true |
In what ways has the functional characterization of BBX proteins in crop species, such as BBX32 in soybean, BBX21 in potato, or BBX24 in Chrysanthemum, advanced our understanding of their potential applications in improving agronomic traits? | PLANT BIOTECHNOLOGY | [
"Solanum tuberosum",
"Glycine max",
"Chrysanthemum"
] | [
"Functional characterization of BBX proteins indicates they only affect flowering time and have no relevance to traits like photosynthesis or yield improvement.",
"The studies have shown that BBX proteins are primarily involved in promoting vegetative growth, with no significant impact on yield or stress tolerance.",
"Research on BBX proteins has demonstrated their role in enhancing stress resilience, yield potential, and improving phenological traits in crops, leading to applications in breeding programs that can increase crop productivity."
] | https://doi.org/10.1104/pp.17.01417 | Other Herbaceous Crops, Spices, Fibers & Weeds | PLANT BIOTECHNOLOGY | 10.1104/pp.17.01417 | 2,018 | 31 | 2 | Plant Physiology | true |
How does BBX24 influence the interaction between DELLAs and PIF4 in the context of shade avoidance? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"BBX24 has no effect on the interaction between DELLAs and PIF4, regardless of light conditions.",
"BBX24 promotes the interaction between DELLAs and PIF4, leading to reduced growth in shaded environments.",
"BBX24 sequesters DELLAs, preventing them from inhibiting PIF4, which enhances cell elongation and growth in response to shade."
] | https://doi.org/10.1038/ncomms7202 | Model Organisms | GENE REGULATION | 10.1038/ncomms7202 | 2,015 | 89 | 2 | Nature Communications | true |
How does UV-B radiation impact Arabidopsis BBX29 expression and its role in plant defense? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"UV-B radiation strongly induces AtBBX29 expression in a UVR8-dependent manner, enhancing the accumulation of phenolic compounds that boost plant resistance to pathogens.",
"UV-B radiation decreases AtBBX29 expression, leading to reduced accumulation of phenolic compounds and increased susceptibility to pathogens.",
"UV-B radiation has no effect on AtBBX29 expression, and it does not influence plant defense mechanisms."
] | https://link.springer.com/article/10.1007/s43630-023-00391-8 | Model Organisms | ENVIRONMENT | 10.1007/s43630-023-00391-8 | 2,023 | 6 | 0 | Photochemical & Photobiological Sciences | true |
In what ways do photoreceptors, such as phytochromes and cryptochromes, interact with light-regulated transcription factors like HY5, BBXs and PIFs to regulate the developmental processes in crops, and how can these interactions be targeted for crop improvement? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"Interactions between photoreceptors and light-regulated transcription factors like HY5, BBXs and PIFs play a crucial role in regulating key developmental processes, such as flowering time and leaf expansion, and can be targeted in breeding programs to enhance crop performance.",
"Photoreceptors and light-regulated transcription factors operate independently of each other, so their interactions do not influence developmental processes in crops.",
"The primary role of photoreceptors is to inhibit light-regulated transcription factors, which leads to decreased growth rates and reduced crop yield across all species."
] | https://doi.org/10.1104/pp.17.01417 | Non-specific | GROWTH AND DEVELOPMENT | 10.1104/pp.17.01417 | 2,018 | 31 | 0 | Plant Physiology | true |
How do ABA sensitivity and stomatal responses differ between BBX21-OE lines and wild-type potato plants? | HORMONES | [
"Solanum tuberosum"
] | [
"BBX21-OE lines exhibit increased sensitivity to ABA, resulting in reduced stomatal openings compared to wild-type plants when both are exposed to ABA.",
"BBX21-OE lines show improved tolerance to ABA, maintaining stomatal openings under lower ABA concentrations, whereas wild-type plants exhibit reduced stomatal apertures when exposed to ABA.",
"There is no difference in ABA sensitivity or stomatal responses between BBX21-OE lines and wild-type plants under ABA treatment."
] | https://doi.org/10.1111/tpj.15499 | Solanaceae & Relatives | HORMONES | 10.1111/tpj.15499 | 2,021 | 18 | 1 | The Plant Journal | true |
What role does the trans-acting small interfering RNA (tasiRNA) pathway play in lateral root development in Arabidopsis thaliana and what are the components involved? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, cytokinins, miR390, TAS3, and their ARFs targets define a regulatory network quantitatively controlling lateral root growth. Mutations affecting the abundance of TAS3-derived tasiRNAs lead to inhibition of lateral root growth. miR390 is induced in response to cytokinins during lateral root initiation and triggers the local production of tasiRNAs. In the lateral root primordium, the tasiARFs enhance the activity of the auxin response factors ARF2, ARF3, and ARF4, thereby inhibiting lateral root initiation. In addition, ARF2, ARF3, and ARF4 are required for proper miR390 expression through negative feedback mechanisms.",
"In Arabidopsis thaliana, auxin, miR173, TAS1, and their targets define a regulatory network quantitatively controlling lateral root initiation. Mutations affecting the abundance of TAS1-derived tasiRNAs lead to quantitative changes in the number of lateral root initiation events. miR173 is induced in response to auxin during lateral root initiation and triggers the local production of tasiRNAs. In the lateral root primordium, the tasiARFs reduce the activity of the auxin response factors ARF2, ARF3, and ARF4, thereby promoting lateral root initiation. In addition, ARF2, ARF3, and ARF4 repress miR173 expression.",
"In Arabidopsis thaliana, auxin, miR390, TAS3, and their ARFs targets define a regulatory network quantitatively controlling lateral root growth. Mutations affecting the abundance of TAS3-derived tasiRNAs lead to quantitative changes in the rate of lateral root growth. miR390 is induced in response to auxin during lateral root initiation and triggers the local production of tasiRNAs. In the lateral root primordium, the tasiARFs reduce the activity of the auxin response factors ARF2, ARF3, and ARF4, thereby promoting lateral root growth. In addition, ARF2, ARF3, and ARF4 are required for proper miR390 expression through positive and negative feedback mechanisms. \n"
] | https://doi.org/10.1105/tpc.109.072553 | Model Organisms | GENE REGULATION | 10.1105/tpc.109.072553 | 2,010 | 486 | 2 | The Plant Cell | true |
By which mechanism has the function of the transcription factor LEAFY evolved in land plants? | EVOLUTION | [
"Arabidopsis thaliana",
"Physcomitrella patens"
] | [
"The plant-specific transcription factor LEAFY is found in all land plants, usually as a single copy gene. While it controls general aspects of the life cycle in the basal plant Physcomitrella patens, it has more specialized functions in flowering plants, where it specifically induces floral fate during the reproductive phase. Changes in the mode of DNA binding of the conserved DNA binding domain of LEAFY underpin this change in function. Structural analyses show that Hornworts have preserved a promiscuous intermediary form able to bind DNA in all conformations, suggesting that this promiscuous intermediate could have smoothed the evolutionary transitions, thereby allowing LEAFY to evolve new binding specificities while remaining a single-copy gene.",
"The plant-specific transcription factor LEAFY is found in all land plants, usually as a small gene family. While it controls general aspects of the life cycle in flowering plants, it has more specialised functions in basal plants, where it specifically induces floral fate during the reproductive phase. Changes in the mode of DNA binding of the variable DNA binding domain of LEAFY underpin this change in function. Structural analyses show that the evolutionary transitions have occurred progressively through the accumulation of several changes.",
"The plant-specific transcription factor LEAFY is found in flowering plants, usually as a single copy gene that controls general aspects of the life cycle. Changes in the variable domains of LEAFY underpin changes in the mode of transcriptional activation."
] | https://doi.org/10.1126/science.1108229 https://doi.org/10.1126/science.1248229 | Model Organisms | EVOLUTION | 10.1126/science.1248229 | 2,014 | 121 | 0 | Science | true |
Where is the biogenesis of trans-acting siRNA taking place in plant cells? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"Trans-acting small interfering RNAs (ta-siRNAs) from the TAS3 precursor are produced by cleavage of the TAS3 precursor by the AGO1/miR173 complex, priming it for conversion into single-stranded RNA by the DICER LIKE 4 (DCL4). AGO7 and DCL4 accumulate in cytoplasmic P-bodies. These foci are membrane-associated sites of accumulation of mRNA primed for degradation. AGO7 congregates with miR390 and DCL4 in the cytoplasm for TAS3 processing.",
"Trans-acting small interfering RNAs (ta-siRNAs) from the TAS3 precursor are produced by cleavage of the TAS3 precursor by the AGO7/miR390 complex, priming it for conversion into double-stranded RNA by the RNA-dependent RNA polymerase RDR6 and SGS3. AGO7, SGS3 and RDR6 accumulate in cytoplasmic foci that are distinct from P-bodies. These foci are membrane-associated sites of accumulation of mRNA stalled during translation. AGO7 congregates with miR390 and SGS3 in membranes and is required in the cytoplasm and membranous siRNA bodies for TAS3 processing.",
"Trans-acting small interfering RNAs (ta-siRNAs) from the TAS3 precursor are produced by cleavage of the TAS3 precursor by the AGO1/miR390 complex, priming it for conversion into double-stranded RNA by the RNA-dependent RNA polymerase RDR2 and SGS3. AGO7, SGS3 and RDR6 accumulate in nuclear foci that are distinct from dicing-bodies. These foci are sites of accumulation of micro-RNA production. AGO7 congregates with miR390 and SGS3 in the nucleus, where it is required for TAS3 processing."
] | https://doi.org/10.1038/emboj.2012.20 | Model Organisms | GENE REGULATION | 10.1038/emboj.2012.20 | 2,012 | 122 | 1 | The EMBO Journal | true |
In Arabidopsis thaliana, what role does the microtubule network play during lateral root initiation and emergence? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"The rearrangement of the microtubule (MT) cytoskeleton, alongside changes in cell-wall properties, contributes to the symmetric radial expansion necessary for endodermis thinning. In the endodermis, the organization and response of the cortical microtubule lattice are polarised. On the inner side, in contact with the pericycle, the arrays are more disorganized than those on the outer side of the same cell. Specific disruption of microtubules in endodermal cells overlying a lateral root primodium results in enhanced cellular remodeling and increased radial swelling of the lateral root primodium. Reorganization of endodermal cortical microtubules depends on a SOLITARY ROOT-dependent auxin response. The MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) is not required for the organization of the endodermal cortical microtubule lattice, the remodelling of the endodermis, and the morphogenesis of the lateral root primordium. Microtubules and MAP70-5 contribute to the swelling of the lateral root primordium outgrowth and together function as an auxin-regulated integrator of mechanical constraints during organogenesis.",
"The rearrangement of the microtubule (MT) cytoskeleton, alongside changes in membrane properties, contributes to the radial expansion necessary for lateral root development. In the endodermis, the organization and response of the cortical microtubule lattice are polarized. On the inner side, in contact with the pericycle, the arrays are disorganized while on the outer side of the same cell, they are organized in parallel arrays. Specific disruption of microtubules in pericycle cells results in delayed cellular remodeling and a flattened lateral root primodium with atypical cell division patterns. Reorganization of pericycle cortical microtubules depends on the MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) which is required for the organization of the pericycle cortical microtubule lattice. Microtubules and MAP70-5 contribute to the lateral root primordium outgrowth and together function as an auxin-regulated driver of growth during organogenesis.",
"The rearrangement of the microtubule (MT) cytoskeleton, alongside changes in cell-wall properties, contributes to the asymmetric radial expansion necessary for lateral root development. In the endodermis, the organization and response of the cortical microtubule lattice are polarized. On the inner side, in contact with the pericycle, the arrays are more ordered than those on the outer side of the same cell. Specific disruption of microtubules in endodermal cells overlying a lateral root primodium results in delayed cellular remodeling and a flattened lateral root primodium with atypical cell division patterns. Reorganization of endodermal cortical microtubules depends on both the swelling of the underlying pericycle and a SHY2-dependent auxin response. The MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) is required for the organization of the endodermal cortical microtubule lattice, the remodelling of the endodermis, and the morphogenesis of the lateral root primordium. Microtubules and MAP70-5 contribute to the perception of lateral root primordium outgrowth by the endodermis and together function as an auxin-regulated integrator of mechanical constraints during organogenesis."
] | https://doi.org/10.1016/j.cub.2019.06.039 https://doi.org/10.1126/sciadv.abm4974 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1126/sciadv.abm4974 | 2,022 | 28 | 2 | Science Advances | true |
What role does TOR play during lateral root formation in Arabidopsis thaliana, and by which mechanism? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"The Target-of-Rapamycin (TOR) kinase plays a crucial role in lateral root (LR) formation in Arabidopsis thaliana by integrating local auxin signaling with systemic metabolic cues. TOR is specifically repressed in the lateral root domain, where it regulates the transcription of key auxin-induced transcription factors, including ARF7, ARF19, and LBD16, all of which are essential for lateral root development. When TOR activity is promoted, LR initiation is enhanced, as the transcription of ARF7, ARF19, and LBD16 is significantly increased. Interestingly, TOR activation induces the translation of WOX11, a factor involved in adventitious root formation and promotes root branching. By coordinating metabolic signals with the transcription of auxin-responsive genes, TOR ensures the proper control of lateral root formation. With TOR, auxin signaling can drive root branching, underscoring its pivotal role in linking metabolism to development.",
"The Target-of-Rapamycin (TOR) kinase plays a crucial role in lateral root (LR) formation in Arabidopsis thaliana by integrating local cytokinin signaling with systemic metabolic cues. TOR is specifically repressed in the lateral root domain, where it enhances the translation of key cytokinin-induced transcription factors, including ARF7, ARF19, and LBD16, all of which are essential for lateral root development. When TOR activity is activated, LR initiation is promoted, as the translation of ARF7, ARF19, and LBD16 is significantly attenuated. Interestingly, TOR activation induces the transcription of WOX11, a factor involved in lateral root formation. However, this induction does not lead to root branching, as TOR remains necessary for the translation of LBD16. By coordinating metabolic signals with the translation of cytokinin-responsive genes, TOR ensures the proper initiation and progression of lateral root formation. Without TOR, cytokinin signaling alone cannot drive root branching, underscoring its pivotal role in linking metabolism to development.",
"The Target-of-Rapamycin (TOR) kinase plays a crucial role in lateral root (LR) formation in Arabidopsis thaliana by integrating local auxin signaling with systemic metabolic cues. TOR is specifically activated in the lateral root domain, where it regulates the translation of key auxin-induced transcription factors, including ARF7, ARF19, and LBD16, all of which are essential for lateral root development. When TOR activity is inhibited, LR initiation is blocked, as the translation of ARF7, ARF19, and LBD16 is significantly attenuated. Interestingly, TOR inhibition induces the transcription of WOX11, a factor involved in adventitious root formation. However, this induction does not lead to root branching, as TOR remains necessary for the translation of LBD16. By coordinating metabolic signals with the translation of auxin-responsive genes, TOR ensures the proper initiation and progression of lateral root formation. Without TOR, auxin signaling alone cannot drive root branching, underscoring its pivotal role in linking metabolism to development."
] | https://doi.org/10.15252/embj.2022111273 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.15252/embj.2022111273 | 2,023 | 27 | 2 | The EMBO Journal | true |
What is ‘state transitions’ and which molecular processes are involved in its regulation in plants? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"State transitions is the process through which plants rebalance the activity of photosystem I (PSI) and photosystem II (PSII) under fluctuating light quality conditions. Two states were defined, one induced by light preferentially absorbed by PSII (State II), and the other induced by light preferentially absorbed by PSI (State I). The transition from one state to the other is triggered by changes in the redox state of the plastoquinone (PQ) pool. Under conditions where PSII is preferentially excited, reduction of the PQ pool activates the STN7/STT7 kinase which phosphorylates the membrane-bound light-harvesting complex II (LHCII). Phosphorylation of LHCII results in its detachment from PSII and attachment to PSI, triggering the transition from State I to State II. Conversely, when the PQ pool gets oxidized due to preferential absorption of light by PSI, the STN7/STT7 kinase is deactivated, and LHCII is dephosphorylated by the TAP38/PPH1 phosphatase. Dephosphorylation triggers migration of LHCII back to PSII, leading to State I transition.",
"State transitions is the process through which plants rebalance the activity of photosystem I (PSI) and photosystem II (PSII) under fluctuating light quality conditions. Two states were defined, one induced by light preferentially absorbed by PSI (State II), and the other induced by light preferentially absorbed by PSII (State I). The transition from one state to the other is triggered by changes in the redox state of the plastoquinone (PQ) pool. Under conditions where PSI is preferentially excited, reduction of the PQ pool activates the STN7/STT7 kinase which phosphorylates the membrane-bound light-harvesting complex II (LHCII). Phosphorylation of LHCII results in its detachment from PSII and attachment to PSI, triggering the transition from State I to State II. Conversely, when the PQ pool gets oxidized due to preferential absorption of light by PSII, the STN7/STT7 kinase is deactivated, and LHCII is dephosphorylated by the TAP38/PPH1 phosphatase. Dephosphorylation triggers migration of LHCII back to PSII, leading to State I transition.",
"State transitions is the process through which plants decreases the energy arriving at both photosystem I and II (PSI and PSII) under fluctuating light quality conditions. Two states were defined, one induced by light preferentially absorbed by PSII (State II), and the other induced by light preferentially absorbed by PSI (State I). The transition from one state to the other is triggered by changes in the redox state of the plastoquinone (PQ) pool. Under conditions where PSI is preferentially excited, oxidation of the PQ pool activates the STN7/STT7 kinase which phosphorylates the membrane-bound light-harvesting complex II (LHCII). Phosphorylation of LHCII results in its detachment from PSII and attachment to PSI, triggering the transition from State I to State II. Conversely, when the PQ pool gets reduced due to preferential absorption of light by PSII, the STN7/STT7 kinase is deactivated, and LHCII is dephosphorylated by the TAP38/PPH1 phosphatase. Dephosphorylation triggers migration of LHCII back to PSII, leading to State I transition."
] | https://doi.org/10.1016/j.bbabio.2010.11.005 | Non-specific | GROWTH AND DEVELOPMENT | 10.1016/j.bbabio.2010.11.005 | 2,011 | 225 | 0 | Biochimica et Biophysica Acta (BBA) - Bioenergetics | true |
How do you explain the rise in transient chlorophyll a fluorescence when leaves are exposed to light based on the QA model? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"Based on the QA model, the increase in transient fluorescence yield is related to the reduction of electron acceptors and the relaxation of fluorescence quenchers in the photosynthetic electron transport chain. Upon light absorption, photosystem II (PSII) chlorophyll P680 reduces QA (a PSII-bound quinone). Reduced QA cannot accept another electron from P680 until oxidation by the following electron carrier molecule QB. This net reduction of QA is the main contributor to the rise in chlorophyll fluorescence observed after light exposure of leaves. However, further fluorescence emission is released by the relaxation of an unknown quencher due to photosystem I (PSI) oxidation. Therefore, the rise in transient chlorophyll fluorescence reflects the interaction of light-excited PSI and PSII. ",
"Based on the QA model, the increase in transient fluorescence yield is related to light-induced conformational changes in the closed photosystem II (PSII) reaction centers. These structural alterations impact the physical and photochemical properties of the PSII core complex, due to charge stabilization at its donor side. This leads to the relaxation of a fluorescence quencher, increasing the chlorophyll fluorescence emission of the photosystem. Therefore, the rise in transient chlorophyll fluorescence reflects structural modifications within PSII.",
"Based on the QA model, the increase in transient fluorescence yield is related to the reduction of electron acceptors in the photosynthetic electron transport chain. Upon light absorption, photosystm II (PSII) chlorophyll P680 reduces QA (a PSII-bound quinone). Reduced QA cannot accept another electron from P680 until oxidation by the following electron carrier molecule QB. During this period, the reaction center is defined as ‘closed’ and cannot drive electron transfer reactions with further excitation energy, being the absorbed energy released as fluorescence. Therefore, the rise in transient chlorophyll fluorescence reflects the QA reduction rates."
] | https://doi.org/10.1093/jxb/erad252 | Non-specific | GROWTH AND DEVELOPMENT | 10.1093/jxb/erad252 | 2,023 | 25 | 2 | Journal of Experimental Botany | true |
Which and where reactive oxygen species (ROS) are produced in the chloroplast photosynthetic electron transport chain and what is defined as photoinhibition? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"The main site of ROS production in the photosynthetic electron transport chain are photosystem I and II (PSI and PSII). Over-excitation of the photosystems mainly generate singlet excited oxygen (1O2*) at the level of PSII and superoxide radicals (O2.-) and hydrogen peroxide (H2O2) at PSI. ROS production in the photosystems can induce oxidative damage and this process is known as photoinhibition.",
"The main site of ROS production in the photosynthetic electron transport chain are photosystem I and II (PSI and PSII). Over-excitation of the photosystems mainly generate singlet excited oxygen (1O2*) at the level of PSI and superoxide radicals (O2.-) and hydrogen peroxide (H2O2) at PSII. ROS production in the photosystems can induce oxidative damage and and this process is known as photoinhibition.",
"The only site of ROS production in the photosynthetic electron transport chain is photosystem II (PSII). Over-excitation of PSII can trigger triplet excited state chlorophylls (3Chl*) which are highly reactive and transfer the energy to oxygen, thereby generating singlet excited oxygen (1O2*). Singlet excited oxygen can induce oxidative damage of the D1 protein in the reaction center and PSII photoinactivation. This process is known as photoinhibition."
] | https://doi.org/10.1042/BST20211246 | Non-specific | GROWTH AND DEVELOPMENT | 10.1042/BST20211246 | 2,022 | 24 | 0 | Biochemical Society Transactions | true |
What is the role of the transporters TPT and PHT2;1 in regulating chloroplastic phosphorus (Pi) homeostasis and photosynthesis in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"TPT and PHT2;1 are molecular transporters that import phosphorus (Pi) to the chloroplast stroma in Arabidopsis thaliana. While TPT couples Pi import with triose phosphate export (produced by photosynthesis) to the cytosol, PHT2;1 imports both Pi and H+/Na+. Although both transporters contribute to stromal Pi homeostasis, the TPT transporter contributes more to stromal Pi concentration in the adaxial mesophyll, while PHT2; 1 contributes more in the abaxial mesophyll. Maintaining Pi homeostasis is fundamental for photosynthesis since low stromal Pi levels reduce photosynthetic efficiency and trigger photoprotection processes.",
"TPT and PHT2;1 are molecular transporters that export phosphorus (Pi) from the chloroplast stroma to the cytosol in Arabidopsis thaliana. While TPT couples Pi and triose phosphate (produced by photosynthesis) export to the cytosol, PHT2;1 exports both Pi and H+/Na+. Although both transporters contribute to stromal Pi homeostasis, the TPT transporter regulates more stromal Pi concentration in the adaxial mesophyll, while PHT2; 1 contributes more in the abaxial mesophyll. Maintaining Pi homeostasis is fundamental for photosynthesis since low stromal Pi levels reduce photosynthetic efficiency and trigger photoprotection processes.",
"TPT and PHT2;1 are molecular transporters that import phosphorus (Pi) to the chloroplast lumen in Arabidopsis thaliana. Although both transporters contribute to stromal Pi homeostasis, the TPT transporter contributes more to the lumen Pi concentration in the abaxial mesophyll, while PHT2; 1 contributes more in the adaxial mesophyll. Maintaining Pi homeostasis in the chloroplast is fundamental for ATP synthesis, which is required for carbon fixation. "
] | https://doi.org/10.1093/plphys/kiae241 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/plphys/kiae241 | 2,024 | 4 | 0 | Plant Physiology | true |
How can the activity of the plastid terminal oxidase (PTOX) be explained by the PSII proximity hypothesis in plants? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"Photosystem II (PSII) and PTOX are located in different sub-compartments of the chloroplast. While PTOX is specifically targeted to the grana, PSII is localized in the stromal lamellae. Since PTOX oxidizes plastoquinol and reduces O2 to produce H2O, its activity will depend on the availability of its substrates. Thus, the distance between PSII and PTOX would preclude a significant electron flow between these two complexes. Decreasing the proximity between PSII and PTOX facilitates electron transport by diffusion of the reduced PQ pool associated with the photosystem.",
"Photosystem II (PSII) and PTOX are located in different sub-compartments of the chloroplast. While PSII is specifically targeted to the grana, PTOX is localized to the stromal lamellae. Since PTOX oxidizes plastoquinol and reduces O2 to produce H2O, its activity will depend on the availability of its substrates. Thus, the distance between PSII and PTOX would preclude a significant electron flow between these two complexes. Decreasing the proximity between PSII and PTOX facilitates electron transport by diffusion of the reduced PQ pool associated with the photosystem.",
"Photosystem II (PSII) and PTOX are located in different sub-compartments of the chloroplast. While PSII is targeted to the grana, PTOX is localized to the stroma. Since PTOX oxidizes plastoquinol (PQ) and reduces O2 to produce H2O, its activity will depend on the availability of its substrates. Thus, the stromal localization of PTOX would preclude a significant oxidation of the PQ pool. Based on the proximity hypothesis, a pH-dependent activation was proposed in which increasing stromal pH triggers PTOX association with the thylakoid membrane. This membrane binding allows electron transport from PSII through the PQ pool to PTOX. "
] | https://doi.org/10.1038/s41467-023-44454-x | Non-specific | GROWTH AND DEVELOPMENT | 10.1038/s41467-023-44454-x | 2,024 | 6 | 1 | Nature Communications | true |
What is the magnitude of alternative splicing regulation in rice leaves undergoing heat stress? | GENE REGULATION - ALTERNATIVE SPLICING | [
"Oryza sativa"
] | [
"Alternative splicing is widespread in rice leaves undergoing heat stress. For instance, genes coding for key regulators of gene expression can be mispliced in response to heat, suggesting that rice leaves are unable to regulate their transcriptome and proteome diversity in response to heat stress. ",
"Alternative splicing regulation is widespread in rice leaves undergoing heat stress. Particularly, genes encoding for key regulators of gene expression undergo heat-stress-induced differential alternative splicing, suggesting that this process helps shape rice leaf transcriptome and proteome diversity in response to heat stress. ",
"Alternative splicing regulation is rare in rice leaves undergoing heat stress. Genes encoding for key regulators of gene expression mostly undergo heat-stress-induced differential gene expression, suggesting that alternative splicing has a small role in shaping rice leaf transcriptome diversity in response to heat stress. "
] | https://doi.org/10.3390/plants10081647 | Model Organisms | GENE REGULATION | 10.3390/plants10081647 | 2,021 | 17 | 1 | Plants | true |
How conserved is the regulation of alternative splicing in circadian clock orthologues from barley and Arabidopsis in response to cold? | GENE REGULATION - ALTERNATIVE SPLICING | [
"Hordeum vulgare",
"Arabidopsis thaliana"
] | [
"The regulation of alternative splicing in circadian clock orthologues shows mostly conserved mechanisms and rarely species-specific divergences between barley and Arabidopsis in response to cold. For example, GI, PRR7 and TOC1 orthologues show conservation of alternative splicing events and behaviour in response to cold. Meanwhile, LHY orthologues show conservation of splicing behaviour, where cold-induced changes in species-specific splicing events lead to a decrease in non-productive transcripts and an increase in functional mRNA levels in both species. ",
"The regulation of alternative splicing in circadian clock orthologues is rarely conserved between barley and Arabidopsis upon cold. For example, GI and TOC1 orthologues have no conserved alternative splicing behaviour. Meanwhile, LHY orthologues show conservation of splicing events, where cold-induced changes in the splicing lead to an increase in non-productive transcripts and a reduction in functional mRNA levels in both species. In contrast, PRR7 orthologues are considerably similar in terms of alternative splicing regulation, with barley (HvPPD-H1) exhibiting temperature-dependent isoform switching, a response also observed in Arabidopsis.",
"The regulation of alternative splicing in circadian clock orthologues shows both conserved mechanisms and species-specific divergences between barley and Arabidopsis upon cold. For example, GI and TOC1 orthologues show conservation of alternative splicing events. Meanwhile, LHY orthologues show conservation of splicing behaviour, where cold-induced changes in species-specific splicing events lead to an increase in non-productive transcripts and a reduction in functional mRNA levels in both species. In contrast, PRR7 orthologues differ markedly, with barley (HvPPD-H1) exhibiting temperature-dependent isoform switching, a response not observed in Arabidopsis"
] | https://doi.org/10.1371/journal.pone.0168028 | Model Organisms | GENE REGULATION | 10.1371/journal.pone.0168028 | 2,016 | 27 | 2 | PLOS ONE | true |
What is the speed of alternative splicing response to cold stress in Arabidopsis leaves? | GENE REGULATION - ALTERNATIVE SPLICING | [
"Arabidopsis thaliana"
] | [
"The alternative splicing response to cold stress in Arabidopsis leaves is rapid. More than half of the genes known to undergo alternative splicing in response to cold show differential gene expression within 9 hours of cold stress. Additionally, over half of the cold-induced isoform switches occurred 6 hours before the cold treatment.",
"The alternative splicing response to cold stress in Arabidopsis leaves is rapid. More than half of the genes known to undergo alternative splicing in response to cold show differential alternative splicing within 9 hours of cold stress. Additionally, over half of the cold-induced isoform switches occurs within 6 hours of cold treatment.",
"The alternative splicing response to cold stress in Arabidopsis leaves is dynamic. Up to half of the genes known to undergo alternative splicing in response to cold show differential alternative splicing 9 hours before the cold stress. Additionally, less than half of the cold-induced isoform switches occurred within 6 hours of cold treatment."
] | https://doi.org/10.1105/tpc.18.00177 | Model Organisms | GENE REGULATION | 10.1105/tpc.18.00177 | 2,018 | 242 | 1 | The Plant Cell | true |
Which is the most comprehensive Reference Transcript Dataset for Arabidopsis thaliana to date? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"AtRTD3 is the most comprehensive and accurate Arabidopsis transcriptome as of 2024. It was constructed from sequencing RNAs from a diverse set of tissues, environmental conditions, and mutants, ensuring transcript diversity. Robust computational methods were used to ensure accuracy of transcript sequences. ",
"TAIR10 is the most comprehensive and accurate Arabidopsis transcriptome of all time. It was constructed from sequencing RNAs from a diverse set of tissues, environmental conditions, and mutants, ensuring transcript diversity. Robust computational methods and manual curation were used to ensure accuracy of transcript sequences. ",
"AtRTD2 is the most comprehensive and accurate Arabidopsis transcriptome to date. It was constructed from sequencing RNA molecules from Arabidopsis rosettes exposed to different environmental conditions, ensuring transcript diversity. Robust computational methods were used to ensure accuracy of transcript sequences. "
] | https://doi.org/10.1186/s13059-022-02711-0 | Model Organisms | GENOME AND GENOMICS | 10.1186/s13059-022-02711-0 | 2,022 | 56 | 0 | Genome Biology | true |
Why is the AtRTD2-QUASI not the most appropriate Reference Transcript Dataset for quantifying Arabidopsis thaliana transcripts with bona fide alternative transcription start site and/or polyadenylation? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"AtRTD2-QUASI is unable to properly quantify the expression for the majority of genes because it is built on the assumption that much of the variation in 5’ and 3’ UTR length of transcripts is likely due to transcripts lacking regulatory regions (i.e., not being full-length). Accordingly, modifying the transcripts in AtRTD2-QUASI to have variable start and end coordinates has impacted the quantification of most isoforms compared to AtRTD2, which does not implement such modifications. On the other hand, AtRTD2 has lost all information on endogenous alternative transcription start and polyadenylation sites, making it unsuitable for analysing these mechanisms.",
"Although it properly quantifies the expression for the majority of genes, AtRTD2-QUASI is built on the assumption that, for the majority of genes, much of the variation in 5’ and 3’ UTR length of transcripts is likely due to incomplete transcripts lacking terminal regions (i.e., not being full-length). Accordingly, modifying the transcripts in AtRTD2-QUASI to have uniform start and end coordinates has improved quantification for most isoforms compared to AtRTD2, which does not implement such modifications. On the other hand, AtRTD2 has lost all information on alternative transcription start and polyadenylation sites, making it unsuitable for analysing these mechanisms.",
"Although it properly quantifies the expression of all Arabidopsis genes, AtRTD2-QUASI is built on the assumption that each and every variation in 5’ and 3’ UTR length of transcripts is likely due to incomplete transcripts lacking intronic regions (i.e., not being full-length). Accordingly, modifying the transcripts in AtRTD2-QUASI to have uniform start and end coordinates has improved quantification of isoforms compared to AtRTD2, which does not implement such modifications. On the other hand, AtRTD2 has included all information on alternative transcription start and polyadenylation sites, making it unsuitable for analysing these mechanisms."
] | https://doi.org/10.1093/nar/gkx267 | Model Organisms | GENOME AND GENOMICS | 10.1093/nar/gkx267 | 2,017 | 234 | 1 | Nucleic Acids Research | true |
How UV-B radiation impacts in the UVR8 photoreceptor protein structure in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"After UV-B radiation, UVR8 is activated via a structural change from a monomer to dimer. The aminoacids tryptophans Trp- 285 and Trp-233 act as chromophores which absorb UV-B leading to conformational changes generating dimer interactions. ",
"After UV-B radiation, UVR8 is activated via a structural change from a dimer to monomer. The aminoacids arginine Arg- 285 and Arg-233, located in the homodimeric interface, act as chromophores which absorb UV-B leading to conformational changes breaking key cross-dimer interactions. ",
"After UV-B radiation, UVR8 is activated via a structural change from a dimer to monomer. The aminoacids tryptophans Trp- 285 and Trp-233, located in the homodimeric interface, act as chromophores which absorb UV-B leading to conformational changes breaking key cross-dimer interactions. "
] | https://doi.org/10.1146/annurev-arplant-050718-095946 | Model Organisms | ENVIRONMENT | 10.1146/annurev-arplant-050718-095946 | 2,021 | 108 | 2 | Annual Review of Plant Biology | true |
How is the E3 ubiquitin ligase COP1 involved in UV-B perception and signalling in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"COP1 forms an E3 ubiquitin ligase complex together with SPA proteins, and this complex represses photomorphogenesis in the dark by directing promoting factors, such as the UV-B photoreceptor UVR8, to be degraded. After UV-B radiation, the TF HY5 interacts with COP1. This interaction sequesters COP1 from the E3 ubiquitin ligase complex, blocking its degradation function. ",
"COP1 forms an E3 ubiquitin ligase complex together with SPA proteins, and this complex represses photomorphogenesis in the dark by directing promoting factors, such as the positive regulator of photomorphogenesis HY5, to be degraded. After UV-B radiation, UVR8 monomer interacts with COP1. This interaction sequesters COP1 from the E3 ubiquitin ligase complex, avoiding HY5 destabilization. ",
"COP1 forms an E3 ubiquitin ligase complex together with SPA proteins, and this complex activates photomorphogenesis by promoting the synthesis of transcription factors such as HY5. After UV-B radiation, UVR8 monomer interacts with COP1. This interaction sequesters COP1 from the E3 ubiquitin ligase complex, impairing HY5 synthesis."
] | https://doi.org/10.1007/s44154-022-00076-9 | Model Organisms | ENVIRONMENT | 10.1007/s44154-022-00076-9 | 2,022 | 44 | 1 | Stress Biology | true |
Which proteins facilitate UVR8 redimerization in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"The proteins are WD40-repeat RUP1 and RUP2 proteins and their transcripts are UV-B inducible in a UVR8 dependent manner. These proteins interact with both UVR8 homodimer and monomers, although they have a stronger affinity for active UVR8 monomers. RUP1 and RUP2 facilitate redimerization of UVR8 in vivo within 2 h to balance the signalling pathway.",
"The proteins are RUP1 and RUP2 proteins and their transcripts are UV-B inducible in a UVR8 dependent manner. These proteins have a strong affinity with COP1 sequestering it from the complex UVR8-COP1 and facilitating the consequent redimerization of UVR8 within 2 h of UV-B exposure to balance the signalling pathway.",
"The proteins are two TF RUP1 and RUP2 which are UV-B inducible in a UVR8 independent manner. These factors interact with both UVR8 homodimer and monomers, although they have a stronger affinity for active UVR8 monomers. RUP1 and RUP2 facilitate redimerization of UVR8 in vivo within 2 h to balance the signalling pathway."
] | https://doi.org/10.1146/annurev-arplant-050718-095946 | Model Organisms | ENVIRONMENT | 10.1146/annurev-arplant-050718-095946 | 2,021 | 108 | 0 | Annual Review of Plant Biology | true |
Which is the subcellular localization and activity of UVR8 in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"UVR8 localizes both in the cytosol and the nucleus. Upon UV-B exposure, UVR8 monomers accumulate in the nucleus, although it does not have a nuclear localization signal (NLS). Intriguingly, COP1 is required for UVR8 nuclear accumulation, and it includes both an NLS and a nuclear export signal. Alternatively, UVR8 may enter the nucleus through either diffusion or its interaction with presently unknown NLS-containing proteins.",
"UVR8 localizes both in the cytosol and the nucleus. Upon UV-B exposure, UVR8 monomers accumulate in the cytosol, although it does not have a nuclear export signal. Intriguingly, COP1 is required for UVR8 cytosol accumulation, and it includes a nuclear export signal. ",
"UVR8 localizes both in the cytosol and the nucleus. Upon UV-B exposure, UVR8 monomers accumulate in the nucleus. UVR8 may enter the nucleus because of a nuclear localization signal (NLS) present in its structure. "
] | https://doi.org/10.1146/annurev-arplant-050718-095946 | Model Organisms | ENVIRONMENT | 10.1146/annurev-arplant-050718-095946 | 2,021 | 108 | 0 | Annual Review of Plant Biology | true |
Which role plays the transcription factor HY5 in UV-B signaling in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"HY5 is a positive regulator of photomorphogenesis, and it directly binds to DNA to regulate expression of numerous genes. HY5 and its homolog HYH, show partially overlapping function in signalling pathways downstream of several photoreceptors; however, HY5 plays the major role under all light conditions. HY5 is also a substrate for the COP1/SPA E3 ubiquitin ligase complex and due to the UVR8–COP1 interaction, HY5 is rapidly post transcriptionally stabilized under UV-B. ",
"HY5 is a repressor of photomorphogenesis, and it directly binds to DNA to block the expression of numerous genes under dark conditions. Upon light + UV-B exposure HY5 is a substrate for the COP1/SPA E3 ubiquitin ligase complex and due to the UVR8–COP1 interaction, HY5 is rapidly post transcriptionally degraded.",
"HY5 is a positive regulator of photomorphogenesis. Under light conditions, it forms a homodimer but after UV-B radiation, HY5 monomerizes and forms a complex with COP1 which binds to DNA to regulate expression of numerous genes, among them, the gene coding for UV-B photoreceptor UVR8. "
] | https://doi.org/10.1146/annurev-arplant-050718-095946 | Model Organisms | ENVIRONMENT | 10.1146/annurev-arplant-050718-095946 | 2,021 | 108 | 0 | Annual Review of Plant Biology | true |
In the framework of alternative splicing, what is an exitron? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"It is a region of an RNA that can be recognized by the spliceosome as an intron but, in opposition to other introns (canonical introns), exitrons have coding capacities and other features that are common for exons. ",
"An exitron is a sequence of DNA that is both an intron and an exon, meaning it has characteristics of both: \nIntron: An intron is a noncoding sequence that is removed before a mature mRNA leaves the nucleus.\nExon: An exon is a coding sequence that is used to create proteins.",
"It is an intron inside a coding exon."
] | 10.1101/gr.186585.114 | Non-specific | GENE REGULATION | 10.1101/gr.186585.114 | 2,015 | 137 | 0 | Genome Research | true |
Considering gene expression in eukaryotes, the definition of the term exitron brings to debate more basic questions related to splicing and alternative splicing, in this sense, what is an intron? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"An intron is a region of an RNA molecule that can be recognized by the spliceosome and spliced out or excised from the RNA molecule forming a lariat. ",
"Is an internal non-coding region of an RNA.",
"It is a segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes."
] | non-specific | Non-specific | GENE REGULATION | null | null | null | 0 | null | true |
Considering the kinetic model that explains the coupling between alternative splicing regulation and RNA polymerase II elongation, a "slower" elongation would favor or not the inclusion of a cassette exon? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"Slower elongation rates of RNA polymerase II are linked to higher exclusion of exon cassettes. ",
"In general a slower elongation rate would favor the inclusion of alternative exons with weak splice sites in their borders. However, there are specific cases in which there is a competition between splice site selection and the binding of a negative regulator, in those cases, a slow transcription rate could favor the exclusion of the specific exon.",
"The kinetic model is not linked to splicing."
] | https://doi.org/10.1016/j.molcel.2014.03.044 | Non-specific | GENE REGULATION | 10.1016/j.molcel.2014.03.044 | 2,014 | 199 | 1 | Molecular Cell | true |
What is the most frequent alternative splicing event in plants? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"In general, the most conspicuous splicing event in plants is intron retention. ",
"Exitron splicing is the most frequent event in plants.",
"Exon skipping. "
] | https://doi.org/10.1016/j.tplants.2019.02.006 | Non-specific | GENE REGULATION | 10.1016/j.tplants.2019.02.006 | 2,019 | 112 | 0 | Trends in Plant Science | true |
There are key differences between plants and animals, also in alternative splicing regulation. In animals the main outcome of alternative splicing of coding genes is the production of proteins with different functions. Would you say that in plants the scenario is the same? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"There are no differences in this sense, the main outcome of alternative splicing is the generation of different isoforms that can be translated to different proteins.",
"The alternative splicing process generates different proteins, in plants as well as in animals.",
"In plants intron retention is the most common alternative splicing outcome. This is related to nuclear retention of the corresponding transcripts. Hence, those transcripts cannot be translated. Furthermore, retained introns tend to have stop codons. As a corollary, the general trend of alternative splicing in plants is to produce isoforms that cannot be translated but could regulate the total output (protein levels) of a gene. "
] | https://doi.org/10.1016/j.tplants.2019.02.006 | Non-specific | GENE REGULATION | 10.1016/j.tplants.2019.02.006 | 2,019 | 112 | 2 | Trends in Plant Science | true |
How are GRF transcription factors regulated, and how do they control leaf growth in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"GRFs are transcriptionally regulated by GIF co-regulators and microRNA miR396 through the transcriptional gene silencing pathway. GRFs control leaf longevity and senescence. An increase in microRNA miR396 reduces GRF expression, inducing senescence and decreasing organ size.",
"GRFs are post-transcriptionally regulated by microRNA miR396 and form protein complexes with GIF co-regulators. GRFs control the transition from stem cells to transit amplifying cells. An increase in microRNA miR396 reduces GRF expression, increasing stem cell numbers and reducing organ size.",
"GRFs are post-transcriptionally regulated by microRNA miR396 and form protein complexes with GIF co-regulators. GRFs control the transition from cell proliferation to cell differentiation in leaves, thereby determining the duration of the proliferative phase. An increase in microRNA miR396 reduces GRF expression, leading to decreased cell proliferation and reduced organ size."
] | 10.1242/dev.043067 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1242/dev.043067 | 2,010 | 443 | 2 | Development | true |
How is the transcription factor ARF2 involved in the control of cell number in Arabidopsis leaves? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"arf2 mutants have larger leaves with more cells. ARF2 directly activates GRF5, a transcription factor that is not regulated by microRNA miR396. Overexpression of GRF5 in arf2 mutants restores the cell number in leaves to wild-type levels.",
"arf2 mutants have larger leaves with more cells. ARF2 directly represses GRF5, a GRF transcription factor that is not regulated by microRNA miR396. A double mutant arf2 grf5 has a similar number of cells as wild-type leaves.",
"arf2 mutants produce larger seeds. The increase in seed size triggers a concomitant increase in leaf size, which in turn activates genes involved in cell proliferation and growth, such as the GRF transcription factors."
] | 10.1093/plphys/kiab014 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/plphys/kiab014 | 2,021 | 30 | 1 | Plant Physiology | true |
What is the function of miR396 in Arabidopsis roots? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"miR396 has well-known functions in leaves, but its roles in other organs, such as roots, have not yet been studied in detail.",
"miR396 controls the transition from cell proliferation to cell differentiation. High levels of miR396 in roots trigger cell differentiation.",
"miR396 controls the transition from stem cells to transit-amplifying cells. High levels of miR396 increase the stemness of the root meristem."
] | 10.1105/tpc.15.00452 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1105/tpc.15.00452 | 2,015 | 141 | 2 | The Plant Cell | true |
How are miRNA precursors recognized by the processing machinery in plant cells? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"All plant miRNA precursors have a 15-nt stem below the miRNA/miRNA* duplex, which is recognized by the DCL1 complex to make the first cut and release a pre-miRNA. The DCL1 complex makes a second cut 21 nucleotides away from the first cut to release the mature microRNA.",
"Plant miRNA precursors can have different structural determinants that guide the DCL1 complex to make the first cut. Precursors may have a 15-nt stem region below the miRNA/miRNA* duplex or a 15-nt stem above the duplex. This allows processing to initiate either from the base of the stem or from the distal loop, respectively.",
"Plant miRNA precursors have an 11-nt stem below the miRNA/miRNA* duplex, which is recognized by DROSHA to release a pre-miRNA. The pre-miRNA is then exported to the cytoplasm, where Dicer makes a second cut."
] | 10.1093/nar/gky853 | Non-specific | GENE REGULATION | 10.1093/nar/gky853 | 2,018 | 15 | 1 | Nucleic Acids Research | true |
Do mismatches in the miRNA/miRNA* region of the precursor impact miRNA precursor processing in Arabidopsis Thaliana? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"No, the only important factor is the presence of an overall double-stranded RNA region in the precursor.",
"Yes, the number and position of mismatches in the miRNA/miRNA* duplex determine whether the miRNA translationally inhibits its target or guides target cleavage.",
"Yes, mismatches can reduce the processing efficiency."
] | 10.1093/nar/gkae458 | Model Organisms | GENE REGULATION | 10.1093/nar/gkae458 | 2,024 | 4 | 2 | Nucleic Acids Research | true |
In Arabidopsis, the long non-coding RNA, SVALKA, represses CBF1 via which molecular mechanism? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"Transcriptional collision",
"Transcriptional regulation",
"Epigenetic regulation"
] | 10.1038/s41467-018-07010-6 | Model Organisms | GENE REGULATION | 10.1038/s41467-018-07010-6 | 2,018 | 177 | 0 | Nature Communications | true |
What is the hallmark of RNAPII collision in Arabidopsis? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"RNAPII stalling on both DNA strands detected by plaNET-seq",
"Prematurely terminated mRNA detected by RNA-seq",
"Increased occurrence of transcription end sites detected by Direct RNA-seq"
] | 10.1038/s41467-018-07010-6 | Model Organisms | GENE REGULATION | 10.1038/s41467-018-07010-6 | 2,018 | 177 | 0 | Nature Communications | true |
Why cannot two RNAPII complexes pass each other when transcribing on opposite DNA strands? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"DNA looping",
"Formation of R-loops",
"Steric hindrance"
] | 10.1016/j.molcel.2012.08.027 | Model Organisms | GENE REGULATION | 10.1016/j.molcel.2012.08.027 | 2,012 | 151 | 2 | Molecular Cell | true |
What is the prerequisite for transcriptional collision? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"Phosphorylation of serine 2 of the NRPB1 CTD-tail",
"Simultaneous transcription of both DNA strands in opposite direction ",
"Increased RNAPII stalling on one DNA strand"
] | 10.1038/s41467-018-07010-6 | Non-specific | GENE REGULATION | 10.1038/s41467-018-07010-6 | 2,018 | 177 | 1 | Nature Communications | true |
Where is the main stalling site in the 5'-end of genes in Arabidopsis? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"The +1 nucleosome",
"The transcription start site",
"100 bp downstream of the transcription start site"
] | 10.1093/nar/gkz1189 | Model Organisms | GENE REGULATION | 10.1093/nar/gkz1189 | 2,019 | 91 | 0 | Nucleic Acids Research | true |
End of preview. Expand
in Data Studio
Dataset Card for MoBiPlant
Dataset Summary
MoBiPlant is a multiple-choice question-answering dataset curated by plant molecular biologists worldwide. It comprises two merged versions:
- Expert MoBiPlant: 565 expert-level questions authored by leading researchers.
- Synthetic MoBiPlant: 1,075 questions generated by large language models from papers in top plant science journals.
Each example consists of a question about plant molecular biology, a set of answer options, and the index of the correct answer. This dataset benchmarks MCQ-based knowledge in models within the plant molecular biology domain.
Dataset Details
- Name: MoBiPlant
- Version: v1.0
- GitHub: https://github.com/manoloFer10/mobiplant
- License: Creative Commons Attribution 4.0 International (CC BY 4.0)
- Release Date: 2025-06-09
Supported Tasks and Leaderboards
The primary task is:
- Multiple-Choice Question Answering: Given a question and a list of answer choices, predict the index of the correct option.
Leaderboard
Benchmark on Expert MoBiPlant (565 questions):
| Model | CoT Answer Accuracy (%) |
|---|---|
| LLaMA 3.1 405B | 77.6 |
| GPT-4o | 81.2 |
| o1-mini | 81.1 |
| deepseek v3 | 84.3 |
| deepseek-r1 | 86.4 |
| Claude 3.5 Sonnet | 88.1 |
| Gemini 1.5 Pro | 76.8 |
For full results on both versions, see the associated paper.
Languages
- Language: English
Dataset Structure
Versions:
- Expert: 565 expert-authored questions.
- Synthetic: 1,075 LLM-generated questions.
Splits:
- The
trainsplit contains all examples (1,640 total). To access each version, see Usage.
- The
Number of Examples:
- 1,640 total examples across expert and synthetic sets.
Data Fields
Each entry in the train split contains:
| Field | Type | Description |
|---|---|---|
question |
string |
The MCQ question text. |
options |
list[string] |
A list of possible answer strings. |
answer |
int |
Index of the correct option in options (0-based). |
area |
string |
General research area (e.g., GENE REGULATION - TRANSLATION). |
normalized_area |
string |
Normalized research area category (e.g., GENE REGULATION). |
plant_species |
list[string] |
Original plant species labels (e.g., ["Arabidopsis thaliana", "Zea mays"]). |
normalized_plant_species |
string |
Normalized plant species label (e.g., Non-specific). |
doi |
string |
DOI of the primary source publication. |
source |
string |
URL or citation of the source article. |
source_journal |
string |
Journal of publication of the source article. |
Year |
int |
Publication year of the source. |
Citations |
int |
Number of citations the source article has received. |
is_expert |
bool |
True if the example belongs to the Expert MoBiPlant subset; False otherwise. |
Usage
from datasets import load_dataset
# Load from HF
mobiplant = load_dataset("manufernandezbur/MoBiPlant")['train']
# Filter out expert and synthetic versions (optional)
expert_mobiplant = mobiplant.filter(lambda question: question['is_expert'])
synth_mobiplant = mobiplant.filter(lambda question: not question['is_expert'])
# Example iteration
for example in expert_mobiplant:
question = example["question"]
options = example["options"]
label = example["answer"]
print(f'Question: {question}')
print('Options: ','\n'.join([ chr(65+i) + opt for i,opt in enumerate(options)]))
print('Correct Answer: ', options[label])
Citation
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