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)
Specialized Center (P50)
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Special Emphasis Panel (ZGM1)
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University of California Berkeley
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McGlincy, Nicholas J; Ingolia, Nicholas T (2017) Transcriptome-wide measurement of translation by ribosome profiling. Methods 126:112-129
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
Iwasaki, Shintaro; Ingolia, Nicholas T (2017) The Growing Toolbox for Protein Synthesis Studies. Trends Biochem Sci 42:612-624
Zubradt, Meghan; Gupta, Paromita; Persad, Sitara et al. (2017) DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat Methods 14:75-82
Wright, Addison V; Liu, Jun-Jie; Knott, Gavin J et al. (2017) Structures of the CRISPR genome integration complex. Science 357:1113-1118
Lintner, Nathanael G; McClure, Kim F; Petersen, Donna et al. (2017) Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain. PLoS Biol 15:e2001882
Cate, Jamie H D (2017) Human eIF3: from 'blobology' to biological insight. Philos Trans R Soc Lond B Biol Sci 372:
Kostova, Kamena K; Hickey, Kelsey L; Osuna, Beatriz A et al. (2017) CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides. Science 357:414-417
Li, Bo; Tambe, Akshay; Aviran, Sharon et al. (2017) PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Syst 4:568-574.e7
Liu, S John; Horlbeck, Max A; Cho, Seung Woo et al. (2017) CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 355:

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