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| Status |
Public on Nov 11, 2016 |
| Title |
Systematic mapping of functional enhancer-promoter connections with CRISPR interference |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| 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.
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| Contributor(s) |
Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM |
| Citation(s) |
27708057 |
| Submission date |
Sep 22, 2016 |
| Last update date |
Nov 01, 2019 |
| Contact name |
Jesse Engreitz |
| Organization name |
Broad Institute
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA343954 |
| SRA |
SRP090317 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE87257_counts.txt.gz |
710.4 Kb |
(ftp)(http) |
TXT |
| GSE87257_hg19_abundant_rnas.fa.gz |
584.8 Kb |
(ftp)(http) |
FA |
| GSE87257_hg19_refseq_annotation.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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