High-throughput mapping of regulatory DNA
Name
High-throughput mapping of regulatory DNA.pdf
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2.67 MB
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Checksum (MD5)
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Author(s)
Kooshesh, Kameron
Banerjee, Budhaditya
Emons, Bart J M
Sherwood, Richard I
Rajagopal, Nisha
Srinivasan, Sharanya
Guo, Yuchun
Edwards, Matthew D
Syed, Tahin Fahmid
Gifford, David K
Date Issued
January 2016
Journal
Nature Biotechnology
Publisher
Nature Publishing Group
Citation
Rajagopal, Nisha; Srinivasan, Sharanya; Kooshesh, Kameron et al. “High-Throughput Mapping of Regulatory DNA.” Nature Biotechnology 34, 2 (January 2016): 167–174 © 2016 Macmillan Publishers Limited, part of Springer Nature
Version
Author's final manuscript
Abstract
Quantifying the effects of cis-regulatory DNA on gene expression is a major challenge. Here, we present the multiplexed editing regulatory assay (MERA), a high-throughput CRISPR-Cas9–based approach that analyzes the functional impact of the regulatory genome in its native context. MERA tiles thousands of mutations across ~40 kb of cis-regulatory genomic space and uses knock-in green fluorescent protein (GFP) reporters to read out gene activity. Using this approach, we obtain quantitative information on the contribution of cis-regulatory regions to gene expression. We identify proximal and distal regulatory elements necessary for expression of four embryonic stem cell–specific genes. We show a consistent contribution of neighboring gene promoters to gene expression and identify unmarked regulatory elements (UREs) that control gene expression but do not have typical enhancer epigenetic or chromatin features. We compare thousands of functional and nonfunctional genotypes at a genomic location and identify the base pair–resolution functional motifs of regulatory elements.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1038/nbt.3468
