Our overall goal is to systematically define c/s-regulatory elements in mRNAs that control miRNA-mediated silencing under defined physiological conditions. While many miRNA targets have been predicted, and some individual targets have been investigated experimentally, the ways in which mRNA structures enhance or inhibit miRNA targeting are not known for the human transcriptome.
We aim to:
Aim 1) Map mlRNA-responsive mRNA structure in human fibroblasts.
Aim 2) Map miR-122-responsive mRNA structure in human liver cells Aim 3) Develop SHAPE-Seq for in vivo cross-validafion and analysis of mRNAs identified in Aims 1 &2.
Aim 4) Develop computafional models for predicfing miRNA target site use and efficacy. Our efforts will focus on developing validated models for miRNA binding site selecfion in human cells, with a long-term goal of coupling general properties of RNA structure to systems-level experimental constraints to enable the predicfion of miRNA targefing patterns.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZGM1)
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University of California Berkeley
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Tambe, Akshay; East-Seletsky, Alexandra; Knott, Gavin J et al. (2018) RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a. Cell Rep 24:1025-1036
Lee, Yeon J; Wang, Qingqing; Rio, Donald C (2018) Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5. Genes Dev 32:1060-1074
Costa, Elizabeth A; Subramanian, Kelly; Nunnari, Jodi et al. (2018) Defining the physiological role of SRP in protein-targeting efficiency and specificity. Science 359:689-692
Jost, Marco; Weissman, Jonathan S (2018) CRISPR Approaches to Small Molecule Target Identification. ACS Chem Biol 13:366-375
Horlbeck, Max A; Xu, Albert; Wang, Min et al. (2018) Mapping the Genetic Landscape of Human Cells. Cell 174:953-967.e22
Friedman, Jonathan R; Kannan, Muthukumar; Toulmay, Alexandre et al. (2018) Lipid Homeostasis Is Maintained by Dual Targeting of the Mitochondrial PE Biosynthesis Enzyme to the ER. Dev Cell 44:261-270.e6
Zhang, Yan; Burkhardt, David H; Rouskin, Silvi et al. (2018) A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation. Mol Cell 70:274-286.e7
Wang, Qingqing; Rio, Donald C (2018) JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns. Proc Natl Acad Sci U S A 115:E8181-E8190
Jost, Marco; Chen, Yuwen; Gilbert, Luke A et al. (2017) Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent. Mol Cell 68:210-223.e6
McGlincy, Nicholas J; Ingolia, Nicholas T (2017) Transcriptome-wide measurement of translation by ribosome profiling. Methods 126:112-129

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