Transcriptomics,Genomics

Dataset Information

147

Systematic mapping of functional enhancer-promoter connections with CRISPR interference


ABSTRACT: Gene expression in mammals is regulated by noncoding elements that can impact physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses CRISPR interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase (Mb) of sequence in the vicinity of 2 essential transcription factors, MYC and GATA1, and identify 9 distal enhancers that control gene expression and cellular proliferation. Quantitative features of chromatin state and chromosome conformation distinguish the 7 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. Overall design: We examined the effects of using CRISPRi to inhibit a putative enhancer of GATA1, eHDAC6. We performed RNA sequencing on K562 cells expressing individual sgRNAs targeting the transcription start site of GATA1 (2 sgRNAs), eHDAC6 (2 sgRNAs) and non-targeting, negative controls (4 sgRNAs). We generated paired-end RNA sequencing libraries from 3 biological replicates for each sgRNA.

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Charles Fulco 

PROVIDER: GSE87257 | GEO | 2016-11-11

SECONDARY ACCESSION(S): PRJNA343954

REPOSITORIES: GEO

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Publications

Systematic mapping of functional enhancer-promoter connections with CRISPR interference.

Fulco Charles P CP   Munschauer Mathias M   Anyoha Rockwell R   Munson Glen G   Grossman Sharon R SR   Perez Elizabeth M EM   Kane Michael M   Cleary Brian B   Lander Eric S ES   Engreitz Jesse M JM  

Science (New York, N.Y.) 20160929 6313


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  ...[more]

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