Introduction

High-throughput protein-RNA interaction data generated by CLIP-seq has provided an unprecedented depth of access to the activities of RNA-binding proteins (RBPs), the key players in co- and post-transcriptional regulation of gene expression. Motif discovery forms part of the necessary follow-up data analysis for CLIP-seq, both to refine the exact locations of RBP binding sites, and to characterize them. The specific properties of RBP binding sites, and the CLIP-seq methods, provide additional information not usually present in the classic motif discovery problem: the binding site structure, and cross-linking induced events in reads. We show that CLIP-seq data contains clear secondary structure signals, as well as technology- and RBP-specific cross-link signals. We introduce Zagros, a motif discovery algorithm specifically designed to leverage this information and explore its impact on the quality of recovered motifs. Our results indicate that using both secondary structure and cross-link modifications can greatly improve motif discovery on CLIP-seq data. Further, the motifs we recover provide insight into the balance between sequence- and structure-specificity struck by RBP binding.

Publications

  1. Leveraging cross-link modification events in CLIP-seq for motif discovery.
    Cite this
    Bahrami-Samani E, Penalva LO, Smith AD, Uren PJ, 2015-01-01 - Nucleic acids research

Credits

  1. Emad Bahrami-Samani
    Developer

    Molecular and Computational Biology, University of Southern California, United States of America

  2. Luiz O F Penalva
    Developer

    Children's Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center

  3. Andrew D Smith
    Developer

    Molecular and Computational Biology, University of Southern California, United States of America

  4. Philip J Uren
    Investigator

    Molecular and Computational Biology, University of Southern California, United States of America

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Summary
AccessionBT006501
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByPhilip J Uren