ArticleNucleic acids research2013
Prediction of clustered RNA-binding protein motif sites in the mammalian genome.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 76 citations in OpenAlex.
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- Clusters of deep intronic RbFox motifs embedded in large assembly of splicing regulators sequences regulate alternative splicing.PLoS genetics · 2025Article
- A deep learning model for characterizing protein-RNA interactions from sequences at single-base resolution.Patterns (New York, N.Y.) · 2025Article
- Human lncRNAs harbor conserved modules embedded in different sequence contexts.Non-coding RNA research · 2024Article
- Role of RNA-binding Proteins in Regulating Cell Adhesion and Progression of the Atherosclerotic Plaque and Plaque Erosion.Current atherosclerosis reports · 2024Review
- Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell genomics · 2024Article
- Choroid plexus mis-splicing and altered cerebrospinal fluid composition in myotonic dystrophy type 1.Brain : a journal of neurology · 2023Article
- Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex.Nature communications · 2023Article
- RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.PLoS computational biology · 2022Article
- Differences in splicing defects between the grey and white matter in myotonic dystrophy type 1 patients.PloS one · 2020Article
- Short Tandem Repeat Expansions and RNA-Mediated Pathogenesis in Myotonic Dystrophy.International journal of molecular sciences · 2019Review
- Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.Molecular cell · 2019Article
- Combinatorial recognition of clustered RNA elements by the multidomain RNA-binding protein IMP3.Nature communications · 2019Article
- Interplay between coding and exonic splicing regulatory sequences.Genome research · 2019Article
- LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs.Molecular cell · 2018Article
- Precise temporal regulation of alternative splicing during neural development.Nature communications · 2018Article
- Myotonic Dystrophy and Developmental Regulation of RNA Processing.Comprehensive Physiology · 2018Review
- SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.PLoS computational biology · 2018Article
- Article
- The combinatorial control of alternative splicing in C. elegans.PLoS genetics · 2017Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
Abstract
Sequence-specific interactions of RNA-binding proteins (RBPs) with their target transcripts are essential for post-transcriptional gene expression regulation in mammals. However, accurate prediction of RBP motif sites has been difficult because many RBPs recognize short and degenerate sequences. Here we describe a hidden Markov model (HMM)-based algorithm mCarts to predict clustered functional RBP-binding sites by effectively integrating the number and spacing of individual motif sites, their accessibility in local RNA secondary structures and cross-species conservation. This algorithm learns and quantifies rules of these features, taking advantage of a large number of in vivo RBP-binding sites obtained from cross-linking and immunoprecipitation data. We applied this algorithm to study two representative RBP families, Nova and Mbnl, which regulate tissue-specific alternative splicing through interacting with clustered YCAY and YGCY elements, respectively, and predicted their binding sites in the mouse transcriptome. Despite the low information content in individual motif elements, our algorithm made specific predictions for successful experimental validation. Analysis of predicted sites also revealed cases of extensive and distal RBP-binding sites important for splicing regulation. This algorithm can be readily applied to other RBPs to infer their RNA-regulatory networks. The software is freely available at http://zhanglab.c2b2.columbia.edu/index.php/MCarts.
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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.