ArticleMolecular cell2014
RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins.
Article in Molecular cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 268 papers.
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Who cites it
268 citing papers in PubMed.
- Decoding RNA-protein interactions using high-throughput methods.RNA biology · 2026Review
- CB1 receptor inhibition restores synaptoneurosomal alternative splicing landscape in fragile X syndrome mice.iScience · 2026Article
- Halting translation by the letter with sequence-selective small molecules.Nature chemical biology · 2026Review
- Massively parallel characterization of RNA G-quadruplex stability and molecular recognition.Nucleic acids research · 2026Article
- REAL-TIME VISUALIZATION OF SPLICEOSOME ASSEMBLY REVEALS BASIC PRINCIPLES OF 3' SPLICE SITE SELECTION.Research square · 2026Article
- The molecular determinants of PABPC-mediated deadenylation rate.bioRxiv : the preprint server for biology · 2026Article
- Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins.The FEBS journal · 2026Review
- Sequence and structure of protein binding sites in RNA impact biomolecular condensates.Molecular biology of the cell · 2026Article
- Two Plasmodium vivax hypnozoite-expressed RNA-binding proteins inhibit liver stage replication.Nature communications · 2026Article
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- Inherent Specificity and Variation Sensitivity as Quantitative Metrics for RBP Binding.bioRxiv : the preprint server for biology · 2026Article
- Augmented prediction of multi-species protein-RNA interactions using evolutionary conservation of RNA-binding proteins.Nature communications · 2026Article
- Detection of a sequence feature for recursive splicing.bioRxiv : the preprint server for biology · 2026Article
- RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning.Nature communications · 2026Article
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- Sequence and structure of protein binding sites in RNA impact biomolecular condensates.bioRxiv : the preprint server for biology · 2026Article
- RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.Nucleic acids research · 2026Article
- PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates.BMC genomics · 2026Article
- Allele-specific alternative polyadenylation links noncoding genetic variation to Alzheimer's disease risk.bioRxiv : the preprint server for biology · 2026Article
- Biochemical principles of miRNA targeting in flies.Nature communications · 2026Article
208 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Specific protein-RNA interactions guide posttranscriptional gene regulation. Here, we describe RNA Bind-n-Seq (RBNS), a method that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs), and its application to the developmental alternative splicing factors RBFOX2, CELF1/CUGBP1, and MBNL1. For each factor, we recovered both canonical motifs and additional near-optimal binding motifs. RNA secondary structure inhibits binding of RBFOX2 and CELF1, while MBNL1 favors unpaired Us but tolerates C/G pairing in motifs containing UGC and/or GCU. Dissociation constants calculated from RBNS data using a novel algorithm correlated highly with values measured by surface plasmon resonance. Motifs identified by RBNS were conserved, were bound and active in vivo, and distinguished the subset of motifs enriched by CLIP-Seq that had regulatory activity. Together, our data demonstrate that RBNS complements crosslinking-based methods and show that in vivo binding and activity of these splicing factors is driven largely by intrinsic RNA affinity.
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