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Series GSE108025 Query DataSets for GSE108025
Status Public on May 31, 2018
Title The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Synovial sarcoma (SS) is defined by the hallmark SS18-SSX fusion oncoprotein, which renders BAF complexes aberrant in two manners: gain of SSX to the SS18 subunit and concomitant loss of BAF47 subunit assembly. Here we demonstrate that SS18-SSX globally hijacks BAF complexes on chromatin to activate a SS transcriptional signature we define using primary tumors and cell lines. Specifically, SS18-SSX retargets BAF complexes from enhancers to broad polycomb domains to oppose PRC2-mediated repression and activate bivalent genes. Upon suppression of SS18-SSX, reassembly of BAF47 restores enhancer activation, but is not required for proliferative arrest. These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.
 
Overall design Synovial sarcoma cell lines (Aska, HSSY2, SYO1) were lentivirally infected with either an shControl or a shSSX vector, selected for 48 hours with puromycin, then grown for 5 days, at which point cells were harvested for ChIP-seq preparation. CRL7250 fibroblast cell line was lentivirally infected with either a V5-SS18 or V5-SS18-SSX expressing vector, selected for 48 hours with puromycin, then grown for 5 days, at which point cells were harvested for ChIP-seq preparation.
 
Contributor(s) Pulice J, Kadoch C
Citation(s) 29861296
Submission date Dec 13, 2017
Last update date Mar 26, 2019
Contact name Cigall Kadoch
Organization name Dana-Farber Cancer Institute
Department Pediatric Oncology
Lab Kadoch Lab
Street address 450 Brookline Avenue
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (53)
GSM2887561 Aska shCt SS18
GSM2887562 Aska shSSX SS18
GSM2887563 Aska shCt BAF155
This SubSeries is part of SuperSeries:
GSE108028 The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma
Relations
BioProject PRJNA422263
SRA SRP126661

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Supplementary file Size Download File type/resource
GSE108025_RAW.tar 24.3 Mb (http)(custom) TAR (of BROADPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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