High-throughput mapping of regulatory DNA
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; ... Show more Show less
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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.
DepartmentMassachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Nature Publishing Group
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
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