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SRX21773666: GSM7780177: TC-32 siNEG, Input, rep 2; Homo sapiens; ChIP-Seq
1 ILLUMINA (NextSeq 2000) run: 34.9M spots, 3.5G bases, 1Gb downloads

External Id: GSM7780177_r1
Submitted by: Functional Genetics, National Cancer Institute, National Institutes of Health
Study: EWSR1::FLI1 fusion oncoproteins' regulation of ETS1 (ChIP-seq)
show Abstracthide Abstract
Ewing sarcomas harbor few mutations beyond the chromosomal translocation that initiates disease and the mechanistic basis for the metastasis of these tumors remains poorly understood. The epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the repressive activities of the EWSR1::FLI1/ERG fusion oncoproteins. Focusing on one of the repressed EWSR1::FLI1/ERG target genes, ETS1, we detected EWSR1::FLI1 binding and a H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1's binding of promoter regions, and we show ETS1 regulates the expression of multiple proteins that function in extracellular matrix organization including TENSIN3 (TNS3). Interestingly, TNS3 expression in EWS tumors significantly correlates with that of ETS1 (0.85, FDR <0.01). TNS3 is a focal adhesion protein that contributes to tumor cell migration by connecting the cytoplasmic tail of integrins to the actin cytoskeleton. EWS cell lines, in which we activated ETS1 expression (CRISPRa) exhibited increased TNS3 expression and a migratory phenotype. Critically, the activated ETS1 EWS cell lines show TNS3 accumulation at leading cell edges, with F-actin cytoskeletal reorganization, a phenotype associated with cell migration. Overall design: Ewing sarcoma cell line (TC-32) was analyzed by ChIP-seq. EWSR1::FLI1 was depleted by transfection with siRNA (siFLI1 and siNeg control).
Sample: TC-32 siNEG, Input, rep 2
SAMN37387574 • SRS18879189 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM7780177
Instrument: NextSeq 2000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: ChIP assays were performed using SimpleChIP plus Enzymatic Chromatin IP kit (9005S; Cell Signaling Technology, Danvers, MA). Briefly, cells were crosslinked with final concentration of 1% formaldehyde for 10 miunites. After quenching, cell lysis and enyzmatically digested, chromatin was sonicated using Branson SFX250 Digital Sonifier (Branson Ultrasonics) to obtain a fragment size of 200 - 900 bp. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Thermo Fisher Scientific). ChIP-seq libraries were using SMARTer ThruPlex TAKARA Library Prep kit following manufacturer's instructions. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplited using 8 cycles on the thermocycler.
Runs: 1 run, 34.9M spots, 3.5G bases, 1Gb
Run# of Spots# of BasesSizePublished
SRR2605746434,875,6493.5G1Gb2024-04-15

ID:
29481597

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