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Series GSE80527 Query DataSets for GSE80527
Status Public on Mar 31, 2017
Title The BET protein BRD2 cooperates with CTCF to enforce a transcriptional boundary
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Role of the bromodomain and extraterminal motif (BET) protein BRD2 in CTCF chromatin occupancy, tested by CRISPR/Cas9-mediated depletion of BRD2 in GATA1-null erythroblasts expressing an inducible GATA1-ER fusion (G1E-ER4). Pharmacologic inhibitors of the BET (bromodomain and extraterminal motif) family of proteins are being explored for the treatment of various diseases, including cancer, yet the individual functions of BET proteins remain unclear. Here we find that BRD2 co-localizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites, whereas BRD2 is dispensable for CTCF occupancy. Genome editing at a CTCF/BRD2 co-occupied site reveals a functional boundary element that upon perturbation results in transcriptional misregulation. Single-molecule RNA FISH reveals that either site-specific CTCF loss or BRD2 depletion increases the correlation in expression of two genes flanking the boundary. Together these findings indicate that BRD2 supports chromatin boundary activity in a CTCF-dependent manner and suggest that pharmacologic BET inhibitors influence gene expression in part by perturbing chromatin domain boundary function.
Overall design GATA1-null erythroblasts expressing GATA1 as a GATA1-ER fusion protein (G1E-ER4) were induced to differentiate by the addition of 100nM estradiol for 24 hours. CTCF occupancy was assessed in wild type G1E-ER4 cells and compared to occupancy in 2 independent G1E-ER4 clonal sub-lines which were engineered with CRISPR/Cas9 to express no detectable BRD2 (C8 = BRD2 KO#1, D = BRD2 KO#2).
Contributor(s) Hsu SC, Blobel GA, Giardine BM
Citation(s) 28388437
Submission date Apr 21, 2016
Last update date May 15, 2019
Contact name Gerd A Blobel
Organization name University of Pennsylvania Children's Hospital of Philadelphia
Department Pediatrics/Hematology
Street address 3615 Civic Center Blvd, ARC 315
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (6)
GSM2129856 G1E-ER4+E2 24 hr input
GSM2129857 CTCF G1E-ER4+E2 24 hr
GSM2129858 D_Brd2KO G1E-ER4+E2 24 hr input
This SubSeries is part of SuperSeries:
GSE95804 The BET protein BRD2 cooperates with CTCF to enforce transcriptional and architectural boundaries
BioProject PRJNA319247
SRA SRP073674

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Supplementary file Size Download File type/resource
GSE80527_RAW.tar 12.7 Gb (http)(custom) TAR (of BIGWIG, BROADPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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