High-resolution interrogation of functional elements in the noncoding genome
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Author(s)
Fontanillas, P.
Sanjana, Neville E
Wright, Jason
Zheng, Kaijie
Shalem, Ophir
Joung, Julia
Cheng, Chia-Wei
Regev, Aviv
Zhang, Feng
Date Issued
September 2016
Journal
Science
Publisher
American Association for the Advancement of Science (AAAS)
Citation
Sanjana, N. E. et al. “High-Resolution Interrogation of Functional Elements in the Noncoding Genome.” Science 353, 6307 (September 2016): 1545–1549 © 2016 American Association for the Advancement of Science
Version
Author's final manuscript
Abstract
The noncoding genome affects gene regulation and disease, yet we lack tools for rapid identification and manipulation of noncoding elements. We developed a CRISPR screen using ∼18,000 single guide RNAs targeting > 700 kilobases surrounding the genes NF1, NF2, and CUL3, which are involved in BRAF inhibitor resistance in melanoma. We find that noncoding locations that modulate drug resistance also harbor predictive hallmarks of noncoding function. With a subset of regions at the CUL3 locus, we demonstrate that engineered mutations alter transcription factor occupancy and long-range and local epigenetic environments, implicating these sites in gene regulation and chemotherapeutic resistance. Through our expansion of the potential of pooled CRISPR screens, we provide tools for genomic discovery and for elucidating biologically relevant mechanisms of gene regulation.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Biology
Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences
McGovern Institute for Brain Research at MIT
Koch Institute for Integrative Cancer Research at MIT
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Creative Commons Attribution-Noncommercial-Share Alike
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DOI of Published Version
https://doi.org/10.1126/SCIENCE.AAF7613
