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

Maria Katsantoni; Erik van Nimwegen; Mihaela Zavolan

doi:10.1186/s13059-023-02913-0

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

Genome Biol. 2023 Apr 17;24(1):77. doi: 10.1186/s13059-023-02913-0.

Authors

Maria Katsantoni^{1

2}, Erik van Nimwegen^{3

4}, Mihaela Zavolan^{5

6}

Affiliations

¹ Biozentrum, University of Basel, 4056, Basel, Switzerland. maria.katsantoni@unibas.ch.
² Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. maria.katsantoni@unibas.ch.
³ Biozentrum, University of Basel, 4056, Basel, Switzerland.
⁴ Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
⁵ Biozentrum, University of Basel, 4056, Basel, Switzerland. mihaela.zavolan@unibas.ch.
⁶ Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. mihaela.zavolan@unibas.ch.

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.

Keywords: Bioinformatics; CLIP; Computational workflow; HNRNPC; PTBP1; PUM2; RBFOX2; RBP; RNA regulation; RNA-binding protein; Reproducible research; Sequence specificity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites / genetics
Protein Binding
RNA* / metabolism
RNA-Binding Proteins* / genetics
RNA-Binding Proteins* / metabolism
Sequence Analysis, RNA

Substances

RNA
RNA-Binding Proteins