ArticleMolecular cell2015
Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus.
Article in Molecular cell, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
63 citing papers in PubMed, 116 citations in OpenAlex.
- Translational control in plants: from basic mechanisms to environmental and developmental responses.The Plant journal : for cell and molecular biology · 2026Review
- Cigarette smoke destabilizes G-quadruplex structures and antagonizes G4-ligand effects in macrophages.Scientific reports · 2025Article
- CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo.Nature structural & molecular biology · 2025Article
- Global analysis of excitotoxicity-induced alterations in RNA structure and RNA-protein binding in neurons.iScience · 2025Article
- Structured 3' UTRs destabilize mRNAs in plants.Genome biology · 2024Article
- LncRNA DANA1 promotes drought tolerance and histone deacetylation of drought responsive genes in Arabidopsis.EMBO reports · 2024Article
- Review
- Cognitive enhancing effects of pazopanib in D‑galactose/ovariectomized Alzheimer's rat model: insights into the role of RIPK1/RIPK3/MLKL necroptosis signaling pathway.Inflammopharmacology · 2023Article
- A systematic benchmark of machine learning methods for protein-RNA interaction prediction.Briefings in bioinformatics · 2023Article
- Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.The Plant cell · 2023Review
- How does precursor RNA structure influence RNA processing and gene expression?Bioscience reports · 2023Review
- Long-range RNA structures in the human transcriptome beyond evolutionarily conserved regions.PeerJ · 2023Article
- Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae.The Plant cell · 2022Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Studies on Viroid Shed Light on the Role of RNA Three-Dimensional Structural Motifs in RNA Trafficking in Plants.Frontiers in plant science · 2022Review
- A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences,Frontiers in plant science · 2022Article
- Dynamic changes in RNA-protein interactions and RNA secondary structure in mammalian erythropoiesis.Life science alliance · 2021Article
- Novel insights into the pervasive role of RNA structure in post-transcriptional regulation of gene expression in plants.Biochemical Society transactions · 2021Review
- Transcription Regulation Through Nascent RNA Folding.Journal of molecular biology · 2021Review
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
Posttranscriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of nuclear RNAs has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approaches to globally profile these features in Arabidopsis seedling nuclei in vivo. We reveal anticorrelated patterns of secondary structure and RBP binding throughout nuclear mRNAs that demarcate sites of alternative splicing and polyadenylation. We also uncover a collection of protein-bound sequence motifs, and identify their structural contexts, co-occurrences in transcripts encoding functionally related proteins, and interactions with putative RBPs. Finally, using these motifs, we find that the chloroplast RBP CP29A also interacts with nuclear mRNAs. In total, we provide a simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.