Most human genes are regulated after they are transcribed, at the level of splicing, mRNA decay, translation, and/or mRNA localization. The specificity of post-transcriptional regulation is driven mostly by the sequence- or structure-specific recognition of RNA by RNA-binding proteins (RBPs). We described an integrated series of efforts organized around a single but broad-reaching aim: SA1. To understand the extent, nature and evolutionary conservation of sequence context effects on RBP binding to RNA motifs. We have recently developed an assay called RNA Bind-n-Seq (RBNS) for comprehensive, quantitative analysis of an RBP?s affinity for RNA. Here, we propose to extend this approach to study the determinants of binding to natural human and mouse 3' UTR sequence by several important RBPs.
Sub aims are directed at understanding how RNA secondary structure impacts RBP binding to cognate motifs, understanding the effects of flanking sequence composition, assessing the conservation of RBP affinity to specific RNA regions, and developing and testing a predictive model of RBP/RNA interaction. The project is expected to yield a deeper understanding of how the sequence and structural context of an RNA motif influence its occupancy and regulatory potential, and insights into the functions of RBPs such as FMRP, hnRNP K, MBNL1 and RBFOX1 that play important roles in development and in diseases such as mental retardation, myotonic dystrophy, autism and cancer.

Public Health Relevance

This project will provide comprehensive resources, tools and concepts for understanding the binding of proteins to RNA. It will also generate comprehensive binding affinity data for several important RNA binding proteins, including factors that play central roles in myotonic dystrophy and fragile X syndrome, and other factors that are implicated in autism and cancer, information which may aid in design of therapies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Bender, Michael T
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Massachusetts Institute of Technology
Schools of Arts and Sciences
United States
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Dominguez, Daniel; Freese, Peter; Alexis, Maria S et al. (2018) Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Mol Cell 70:854-867.e9
Pai, Athma A; Paggi, Joseph M; Yan, Paul et al. (2018) Numerous recursive sites contribute to accuracy of splicing in long introns in flies. PLoS Genet 14:e1007588
Pai, Athma A; Henriques, Telmo; McCue, Kayla et al. (2017) The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. Elife 6:
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Wang, Eric T; Ward, Amanda J; Cherone, Jennifer M et al. (2015) Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Res 25:858-71
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Lambert, Nicole; Robertson, Alex; Jangi, Mohini et al. (2014) RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol Cell 54:887-900

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