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

View ORCID ProfileMaria Katsantoni, View ORCID ProfileErik van Nimwegen, View ORCID ProfileMihaela Zavolan
doi: https://doi.org/10.1101/2022.07.06.498949
Maria Katsantoni
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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  • For correspondence: maria.katsantoni@unibas.ch mihaela.zavolan@unibas.ch
Erik van Nimwegen
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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Mihaela Zavolan
1Biozentrum, University of Basel, Basel, 4056, Switzerland
2Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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  • For correspondence: maria.katsantoni@unibas.ch mihaela.zavolan@unibas.ch
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Abstract

Crosslinking and immunoprecipitation (CLIP) is used to determine the transcriptome-wide binding sites of RNA-binding proteins (RBPs). Here we present RCRUNCH, an end-to-end solution to CLIP data analysis that enables the reproducible identification of binding sites as well as the inference of RBP sequence specificity. 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. Furthermore, RCRUNCH 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. RCRUNCH is available at: https://github.com/zavolanlab/RCRUNCH.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/zavolanlab/RCRUNCH

  • Abbreviations

    AAE
    Alu antisense element
    AS
    alignment score
    cDNA
    complementary DNA
    ChIP
    chromatin immunoprecipitation
    CLIP
    crosslinking and immunoprecipitation (CLIP)
    DNA
    deoxyribonucleic acid
    FAIR principles
    findable, accessible, interoperable, reusable
    FDR
    False discovery rate
    mRNA
    messenger RNA
    ncRNA
    non-coding RNA
    PCR
    polymerase chain reaction
    PWM
    positional weight matrix
    RBDs
    RNA-binding domains
    RBPs
    RNA-binding proteins
    RIC
    RNA-interactome capture
    RNA
    ribonucleic acid
    RNA-seq
    RNA sequencing
    RNPs
    ribonucleoprotein complexes
    UMI
    unique molecular identifier
    rRNA
    ribosomal RNA
    tRNA
    transfer RNA
    snRNA
    small nuclear RNA
    SMI
    size-matched input
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    Posted July 06, 2022.
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    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
    bioRxiv 2022.07.06.498949; doi: https://doi.org/10.1101/2022.07.06.498949
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    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
    bioRxiv 2022.07.06.498949; doi: https://doi.org/10.1101/2022.07.06.498949

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