Systematic mapping of functional enhancer-promoter connections with CRISPR interference

Gene expression in mammals is regulated by noncoding elements that can affect physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses clustered regularly interspaced short palindromic repeats (CRISPR) inter...

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Bibliographic Details
Published in:Science (American Association for the Advancement of Science) Vol. 354; no. 6313; pp. 769 - 773
Main Authors: Fulco, Charles P, Munschauer, Mathias, Anyoha, Rockwell, Munson, Glen, Grossman, Sharon R, Perez, Elizabeth M, Kane, Michael, Cleary, Brian, Lander, Eric S, Engreitz, Jesse M
Format: Journal Article
Language:English
Published: United States 11.11.2016
Subjects:
Cell Proliferation - genetics
Chromosome Mapping - methods
Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR-Cas Systems
Disease - genetics
Enhancer Elements, Genetic - genetics
Enhancer Elements, Genetic - physiology
GATA1 Transcription Factor - genetics
Gene Expression Regulation
High-Throughput Nucleotide Sequencing - methods
Humans
K562 Cells
Promoter Regions, Genetic - genetics
Promoter Regions, Genetic - physiology
Proto-Oncogene Proteins c-myc - genetics
Real-Time Polymerase Chain Reaction
ISSN:1095-9203
Online Access:Get more information
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Summary:Gene expression in mammals is regulated by noncoding elements that can affect physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase of sequence in the vicinity of two essential transcription factors, MYC and GATA1, and identify nine distal enhancers that control gene expression and cellular proliferation. Quantitative features of chromatin state and chromosome conformation distinguish the seven enhancers that regulate MYC from other elements that do not, suggesting a strategy for predicting enhancer-promoter connectivity. This CRISPRi-based approach can be applied to dissect transcriptional networks and interpret the contributions of noncoding genetic variation to human disease.
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ISSN:1095-9203
DOI:10.1126/science.aag2445