ArticleNature communications2020
RNA structure-wide discovery of functional interactions with multiplexed RNA motif library.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 27 citations in OpenAlex.
- RNA-binding landscape of amiloride: large-scale profiling and structural basis of U-U mismatch recognition.RSC chemical biology · 2026Article
- RNA-binding proteins: a comprehensive review of multifaceted regulatory mechanisms in neuroinflammation and implications in the pathogenesis of neurological disorders.Journal of neuroinflammation · 2026Review
- Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders.Briefings in bioinformatics · 2025Article
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.Nature communications · 2025Article
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.bioRxiv : the preprint server for biology · 2025Article
- Deep learning-based investigation of chloroplast translation regulatory sequences.Frontiers in plant science · 2025Article
- NaP-TRAP reveals the regulatory grammar in 5'UTR-mediated translation regulation during zebrafish development.Nature communications · 2024Article
- Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.Nucleic acids research · 2024Article
- Unveiling RNA structure-mediated regulations of RNA stability in wheat.Nature communications · 2024Article
- Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries.Communications chemistry · 2024Article
- An interpretable RNA foundation model for exploring functional RNA motifs in plants.Nature machine intelligence · 2024Article
- G-quadruplexes from non-coding RNAs.Journal of molecular medicine (Berlin, Germany) · 2023Review
- Review
- Multi-omics approach reveals posttranscriptionally regulated genes are essential for human pluripotent stem cells.iScience · 2022Article
- Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST.Methods in molecular biology (Clifton, N.J.) · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biochemical assays and computational analyses have discovered RNA structures throughout various transcripts. However, the roles of these structures are mostly unknown. Here we develop folded RNA element profiling with structure library (FOREST), a multiplexed affinity assay system to identify functional interactions from transcriptome-wide RNA structure datasets. We generate an RNA structure library by extracting validated or predicted RNA motifs from gene-annotated RNA regions. The RNA structure library with an affinity enrichment assay allows for the comprehensive identification of target-binding RNA sequences and structures in a high-throughput manner. As a proof-of-concept, FOREST discovers multiple RNA-protein interaction networks with quantitative scores, including translational regulatory elements that function in living cells. Moreover, FOREST reveals different binding landscapes of RNA G-quadruplex (rG4) structures-binding proteins and discovers rG4 structures in the terminal loops of precursor microRNAs. Overall, FOREST serves as a versatile platform to investigate RNA structure-function relationships on a large scale.
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Registered trials
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