NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE83725 Query DataSets for GSE83725
Status Public on Apr 27, 2017
Title PAX3-FOXO1 establishes myogenic super enhancers and recruits BRD4 de novo [7250 ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The fusion transcription factor PAX3-FOXO1 drives oncogenesis in a subset of rhabdomyosarcomas, however the mechanisms by which it remodels chromatin are unknown. We find PAX3-FOXO1 reprograms the cis-regulatory landscape by inducing super enhancers (SEs), in collaboration with master transcription factors MYOG, MYOD and MYCN. This myogenic SE circuitry is consistent across cell lines and primary tumors. Deregulation of PAX3-FOXO1 itself occurs by translocation-induced chromatin loops bringing the PAX3 promoter under the control of FOXO1 enhancers. Protein targets induced by, or bound to, PAX3-FOXO1 occupied SEs, were selectively sensitive to small molecule inhibition. PAX3-FOXO1 co-binds BRD4 at SEs, and BET bromodomains are required for PAX3-FOXO1-dependent transcription and cancer cell growth.
 
Overall design Genome-wide profiles for histone mark H3K27ac, DNase hypersensitivity, PAX3-FOXO1 and coactivator BRD4 in fibroblast cells stably transduced with either empty vector or PAX3-FOXO1 vector.
 
Contributor(s) Gryder BE, Wen X
Citation(s) 28446439
Submission date Jun 26, 2016
Last update date May 15, 2019
Contact name Javed Khan
E-mail(s) khanjav@mail.nih.gov
Phone 2407606135
Organization name NCI, NIH
Department Genetics Branch
Lab Javed Khan
Street address 37 Convent Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (14)
GSM2214071 7250-empty DNase rep1
GSM2214072 7250-empty DNase rep2
GSM2214073 7250-empty DNase rep3
This SubSeries is part of SuperSeries:
GSE83728 Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma
Relations
BioProject PRJNA326874
SRA SRP077231

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83725_RAW.tar 3.8 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap