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Series GSE185127 Query DataSets for GSE185127
Status Public on Aug 15, 2022
Title EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (CUT&Tag II)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.
Overall design EWS/FLI knock-down with RNAi followed by rescue of EWS/FLI expression with a 3XFLAG tagged EWS/FLI cDNA construct
Contributor(s) Showpnil IA, Lessnick SL
Citation(s) 36124657
Submission date Sep 30, 2021
Last update date Oct 26, 2022
Contact name Iftekhar Ahmed Showpnil
Organization name Nationwide Children's Hospital
Department CCCBD
Lab Lessnick
Street address 700 Childrens Drive
City Columbus
State/province OH
ZIP/Postal code 43205
Country USA
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (20)
GSM5606824 A673-EFEndo-CTCF-CUT&Tag 1
GSM5606825 A673-EFEndo-CTCF-CUT&Tag 2
GSM5606826 A673-EFEndo-Rabbit-IgG-CUT&Tag 1
This SubSeries is part of SuperSeries:
GSE185132 EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma
BioProject PRJNA767689
SRA SRP339579

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 204.5 Mb (ftp)(http) BW 201.0 Mb (ftp)(http) BW 171.1 Mb (ftp)(http) BW
GSE185127_CTCF_KDb_peaks_uniq.bed.gz 1.1 Kb (ftp)(http) BED
GSE185127_CTCF_WTb_peaks_uniq.bed.gz 1.0 Kb (ftp)(http) BED
GSE185127_CTCF_stableb_peaks_uniq.bed.gz 31.0 Kb (ftp)(http) BED 420.1 Mb (ftp)(http) BW 311.9 Mb (ftp)(http) BW 329.6 Mb (ftp)(http) BW 154.6 Mb (ftp)(http) BW 139.9 Mb (ftp)(http) BW
GSE185127_peaks_A673_iEF_197_CTCF.narrowPeak.gz 666.1 Kb (ftp)(http) NARROWPEAK
GSE185127_peaks_A673_iEF_714_CTCF.narrowPeak.gz 680.3 Kb (ftp)(http) NARROWPEAK
GSE185127_peaks_A673_iLuc_197_CTCF.narrowPeak.gz 656.5 Kb (ftp)(http) NARROWPEAK
GSE185127_peaks_TC71_iEF_CTCF.narrowPeak.gz 681.8 Kb (ftp)(http) NARROWPEAK
GSE185127_peaks_TC71_iLuc_CTCF.narrowPeak.gz 677.2 Kb (ftp)(http) NARROWPEAK
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Processed data are available on Series record

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