ArticleGenome biology2017
Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 165 citations in OpenAlex.
- CRK2 modulates flowering in Arabidopsis together with GLYCINE-RICH RNA-BINDING PROTEIN 7.The New phytologist · 2026Article
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- Site-specific phosphorylation of LRP regulatesScience advances · 2026Article
- Article
- Genome-Wide Isoform Switching Reveals SR45-Mediated Splicing Control ofInternational journal of molecular sciences · 2025Article
- Long Noncoding RNAs as Emerging Regulators of Seed Development, Germination, and Senescence.International journal of molecular sciences · 2025Review
- The compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIP.Scientific data · 2025Article
- At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.The New phytologist · 2025Article
- Unveiling the regulatory role of GRP7 in ABA signal-mediated mRNA translation efficiency regulation.Nature communications · 2025Article
- The chloroplast RNA-binding protein CP29A supportsProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Regulation of Shade Avoidance Under Low-Blue-Light by MTA in Soybean.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Microbial iCLIP2: enhanced mapping of RNA-protein interaction by promoting protein and RNA stability.RNA (New York, N.Y.) · 2025Article
- Transcriptome and translatome profiling of Col-0 and grp7grp8 under ABA treatment in Arabidopsis.Scientific data · 2024Article
- ALBA proteins facilitate cytoplasmic YTHDF-mediated reading of m6A in Arabidopsis.The EMBO journal · 2024Article
- A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato.Nucleic acids research · 2024Article
- Assessing the Role ofPlants (Basel, Switzerland) · 2024Article
- RNA-Binding Protein-Mediated Alternative Splicing Regulates Abiotic Stress Responses in Plants.International journal of molecular sciences · 2024Review
- The glycine-rich domain of GRP7 plays a crucial role in binding long RNAs and facilitating phase separation.Scientific reports · 2024Article
- Revealing the Arabidopsis AtGRP7 mRNA binding proteome by specific enhanced RNA interactome capture.BMC plant biology · 2024Article
- Arginine methylation of SM-LIKE PROTEIN 4 antagonistically affects alternative splicing during Arabidopsis stress responses.The Plant cell · 2024Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFunctions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) genome-wide to determine the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7.
resultsiCLIP identifies 858 transcripts with significantly enriched crosslink sites in plants expressing AtGRP7-GFP that are absent in plants expressing an RNA-binding-dead AtGRP7 variant or GFP alone. To independently validate the targets, we performed RNA immunoprecipitation (RIP)-sequencing of AtGRP7-GFP plants subjected to formaldehyde fixation. Of the iCLIP targets, 452 were also identified by RIP-seq and represent a set of high-confidence binders. AtGRP7 can bind to all transcript regions, with a preference for 3' untranslated regions. In the vicinity of crosslink sites, U/C-rich motifs are overrepresented. Cross-referencing the targets against transcriptome changes in AtGRP7 loss-of-function mutants or AtGRP7-overexpressing plants reveals a predominantly negative effect of AtGRP7 on its targets. In particular, elevated AtGRP7 levels lead to damping of circadian oscillations of transcripts, including DORMANCY/AUXIN ASSOCIATED FAMILY PROTEIN2 and CCR-LIKE. Furthermore, several targets show changes in alternative splicing or polyadenylation in response to altered AtGRP7 levels.
conclusionsWe have established iCLIP for plants to identify target transcripts of the RNA-binding protein AtGRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues.
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