Genomics

Dataset Information

240

Genome-wide chromatin analysis of Ewing sarcoma (ATAC-seq)


ABSTRACT: We show that EWS-FLI1, an aberrant transcription factor responsible for the pathogenesis of Ewing sarcoma, reprograms gene regulatory circuits by directly inducing or directly repressing enhancers. At GGAA repeats, which lack regulatory potential in other cell types and are not evolutionarily conserved, EWS- FLI1 multimers potently induce chromatin opening, recruit p300 and WDR5, and create de novo enhancers. GGAA repeat enhancers can loop to physically interact with target promoters, as demonstrated by chromosome conformation capture assays. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors and abrogating p300 recruitment. Mesenchymal stem cells (MSCs) and a Ewing sarcoma cell line (SKNMC) were analyzed by ATAC-seq. EWS-FLI1 was expressed in MSCs using a lentiviral vector (pLIV EWSFLI1 or pLIV empty vector control). * Raw data not provided for the MSC samples. *

ORGANISM(S): Homo sapiens  

SUBMITTER: Miguel Rivera   Martin Aryee 

PROVIDER: E-GEOD-61951 | ArrayExpress | 2014-10-30

SECONDARY ACCESSION(S): GSE61951SRP048563PRJNA262779

REPOSITORIES: GEO, ArrayExpress, ENA

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