ArticleGenome biology2023
Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- Immiscible proteins compete for RNA binding to order condensate layers.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- Thermodynamic coupling of the tandem RRM domains of hnRNP A1 underlie its pleiotropic RNA binding functions.Science advances · 2024Article
- Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.STAR protocols · 2024Article
- Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila.BMC biology · 2023Article
- Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.Cell genomics · 2023Article
- Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs.Genome biology · 2023Article
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Authors and funding
3 authors.
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Abstract
We present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not only reads that map uniquely to the genome but also those that map to multiple genome locations or across splice boundaries and can consider various types of background in the estimation of read enrichment. By applying RCRUNCH to the eCLIP data from the ENCODE project, we have constructed a comprehensive and homogeneous resource of in-vivo-bound RBP sequence motifs. RCRUNCH automates the reproducible analysis of CLIP data, enabling studies of post-transcriptional control of gene expression.
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