Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites
Autor: | Justin Wong, Adrian R. Krainer, Huijuan Feng, Aziz Khan, Ankeeta Shah, Mohammad Alinoor Rahman, Suying Bao, Chaolin Zhang, Sebastien M. Weyn-Vanhentenryck, Elise D. Flynn |
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Jazyk: | angličtina |
Rok vydání: | 2019 |
Předmět: |
Models
Molecular Protein Conformation alpha-Helical Immunoprecipitation Gene Expression RNA-binding protein Computational biology Biology Article 03 medical and health sciences 0302 clinical medicine SR protein Sequence Homology Nucleic Acid Humans Heterogeneous Nuclear Ribonucleoprotein D0 Protein Interaction Domains and Motifs Binding site Heterogeneous-Nuclear Ribonucleoprotein D Molecular Biology 030304 developmental biology 0303 health sciences Binding Sites Base Sequence Serine-Arginine Splicing Factors Alternative splicing RNA Cell Biology Hep G2 Cells Cross-Linking Reagents RNA splicing Nucleic Acid Conformation Protein Conformation beta-Strand Sequence motif K562 Cells Sequence Alignment 030217 neurology & neurosurgery HeLa Cells Protein Binding |
Popis: | RNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence motifs in their target transcripts, but precisely defining their binding specificity remains challenging. Crosslinking and immunoprecipitation (CLIP) allows for mapping of the exact protein-RNA crosslink sites, which frequently reside at specific positions in RBP motifs, at single-nucleotide resolution. Here, we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the discovered motifs by genome-wide analysis of allelic binding sites. Our analyses revealed that the prototypical SR protein SRSF1 recognizes clusters of GGA half sites in addition to its canonical GGAGGA motif. Therefore, SRSF1 regulates splicing of a much larger repertoire of transcripts than previously appreciated, including HNRNPD and HNRNPDL, which are involved in multivalent protein assemblies and phase separation. |
Databáze: | OpenAIRE |
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