Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

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 a...

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Autores principales: Katsantoni, Maria, van Nimwegen, Erik, Zavolan, Mihaela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108518/
https://www.ncbi.nlm.nih.gov/pubmed/37069586
http://dx.doi.org/10.1186/s13059-023-02913-0
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author Katsantoni, Maria
van Nimwegen, Erik
Zavolan, Mihaela
author_facet Katsantoni, Maria
van Nimwegen, Erik
Zavolan, Mihaela
author_sort Katsantoni, Maria
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02913-0.
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spelling pubmed-101085182023-04-18 Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs Katsantoni, Maria van Nimwegen, Erik Zavolan, Mihaela Genome Biol Method 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02913-0. BioMed Central 2023-04-17 /pmc/articles/PMC10108518/ /pubmed/37069586 http://dx.doi.org/10.1186/s13059-023-02913-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Katsantoni, Maria
van Nimwegen, Erik
Zavolan, Mihaela
Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
title Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
title_full Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
title_fullStr Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
title_full_unstemmed Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
title_short Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
title_sort improved analysis of (e)clip data with rcrunch yields a compendium of rna-binding protein binding sites and motifs
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108518/
https://www.ncbi.nlm.nih.gov/pubmed/37069586
http://dx.doi.org/10.1186/s13059-023-02913-0
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