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Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites

Huijuan Feng, Suying Bao, Sebastien M. Weyn-Vanhentenryck, Aziz Khan, Justin Wong, Ankeeta Shah, Elise D. Flynn, Chaolin Zhang
doi: https://doi.org/10.1101/428615
Huijuan Feng
1Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York NY 10032, USA
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Suying Bao
1Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York NY 10032, USA
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Sebastien M. Weyn-Vanhentenryck
1Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York NY 10032, USA
2Stoke Therapeutics, Inc, Bedford, MA 01730, USA
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Aziz Khan
3Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
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Justin Wong
1Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York NY 10032, USA
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Ankeeta Shah
1Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York NY 10032, USA
4Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA
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Elise D. Flynn
1Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York NY 10032, USA
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Chaolin Zhang
1Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York NY 10032, USA
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  • For correspondence: cz2294@columbia.edu
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Abstract

RNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence elements in their target transcripts. Despite the expanding list of RBPs with in vivo binding sites mapped genomewide using crosslinking and immunoprecipitation (CLIP), defining precise RBP binding specificity remains challenging. We previously demonstrated that the exact protein-RNA crosslink sites can be mapped using CLIP data at single-nucleotide resolution and observed that crosslinking frequently occurs at specific positions in RBP motifs. 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 resulting motifs by genome-wide analysis of allelic binding sites also detected by CLIP. We found that the prototypical SR protein SRSF1 recognizes GGA clusters to regulate splicing in a much larger repertoire of transcripts than previously appreciated.

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Posted September 27, 2018.
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Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites
Huijuan Feng, Suying Bao, Sebastien M. Weyn-Vanhentenryck, Aziz Khan, Justin Wong, Ankeeta Shah, Elise D. Flynn, Chaolin Zhang
bioRxiv 428615; doi: https://doi.org/10.1101/428615
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Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites
Huijuan Feng, Suying Bao, Sebastien M. Weyn-Vanhentenryck, Aziz Khan, Justin Wong, Ankeeta Shah, Elise D. Flynn, Chaolin Zhang
bioRxiv 428615; doi: https://doi.org/10.1101/428615

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