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Series GSE70671 Query DataSets for GSE70671
Status Public on Oct 19, 2015
Title Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Epigenome editing with the CRISPR/Cas9 platform is a promising technology to modulate gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms that direct gene regulation. Fusions of the nuclease-inactive dCas9 to the KRAB repressor domain (dCas9-KRAB) can effectively silence target gene expression. We targeted dCas9-KRAB to the HS2 enhancer, a distal regulatory element that orchestrates the expression of multiple globin genes. Genome-wide analyses demonstrated that localization of dCas9-KRAB to HS2 specifically induced H3K9 tri-methylation (H3K9me3) at that enhancer and reduced the chromatin accessibility of both the enhancer and its promoter targets. Targeted epigenetic modification of HS2 silenced the expression of multiple globin genes, with minimal off-target changes in gene expression. These results demonstrate that repression mediated by dCas9-KRAB is sufficiently specific to disrupt the activity of individual enhancers via local modification of the epigenome. This approach enables precise modulation of epigenetic function without modifying the underlying genome sequence.
Overall design K562 cells were transduced with in triplicate lentivirus encoding dCas9-KRAB with gRNA targeted to the HS2 globin enhancer. Cells transduced with dCas9-KRAB without gRNA or dCas9 with gRNA targeted to the HS2 globin enhancer were included as controls. RNA-seq was used to identify differential expression at on-target and off-target sites. ChIP-seq was used to identify dCas9-KRAB occupancy and H3K9me3 changes, and DNase-seq was used to identify changes in chromatin accessibility.
Contributor(s) Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NS, Kabadi AM, Crawford GE, Reddy TE, Gersbach CA
Citation(s) 26501517
Submission date Jul 09, 2015
Last update date May 15, 2019
Contact name Mudit Chaand
Organization name Syros Pharmaceuticals
Street address 35 Cambridgepark Drive
City Cambridge
State/province MA
ZIP/Postal code 02140
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (30)
GSM1819865 dCas9_KRAB_FLAG_rep1
GSM1819866 dCas9_KRAB_FLAG_rep2
GSM1819867 dCas9_KRAB_FLAG_rep3
BioProject PRJNA289627
SRA SRP060704

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GSE70671_RAW.tar 6.1 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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