|
| Status |
Public on Aug 15, 2022 |
| Title |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (CuT&Tag I) |
| 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 and EWS/ERG CUT&Tag in A673, TC71, SK-N-MC, EWS-502 and TTC-466 Ewing sarcoma cells
|
| |
|
| 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 |
| E-mail(s) |
[email protected]
|
| 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)
|
|
| This SubSeries is part of SuperSeries: |
| GSE185132 |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma |
|
| Relations |
| BioProject |
PRJNA767688 |
| SRA |
SRP339578 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE185126_A673EEts_EndoGainedEnh_uniq.bed.gz |
19.3 Kb |
(ftp)(http) |
BED |
| GSE185126_A673EEts_EndoLostEnh_uniq.bed.gz |
4.0 Kb |
(ftp)(http) |
BED |
| GSE185126_A673EEts_EndostableEnh_uniq.bed.gz |
26.8 Kb |
(ftp)(http) |
BED |
| GSE185126_A673EEts_RescueGainedEnh_uniq.bed.gz |
11.9 Kb |
(ftp)(http) |
BED |
| GSE185126_A673EEts_RescueLostEnh_uniq.bed.gz |
4.1 Kb |
(ftp)(http) |
BED |
| GSE185126_A673EEts_RescuestableEnh_uniq.bed.gz |
31.3 Kb |
(ftp)(http) |
BED |
| GSE185126_A673_EEts_MS_uniq.bed.gz |
14.3 Kb |
(ftp)(http) |
BED |
| GSE185126_A673_EEts_nonMS_uniq.bed.gz |
34.6 Kb |
(ftp)(http) |
BED |
| GSE185126_A673_EEts_uniq.bed.gz |
142.4 Kb |
(ftp)(http) |
BED |
| GSE185126_A673log2FLIvsIgG10.bw |
197.2 Mb |
(ftp)(http) |
BW |
| GSE185126_AB_endokd_EF_uniq.bed.gz |
535 b |
(ftp)(http) |
BED |
| GSE185126_AB_rskd_EF_uniq.bed.gz |
440 b |
(ftp)(http) |
BED |
| GSE185126_BA_endokd_EF_uniq.bed.gz |
6.0 Kb |
(ftp)(http) |
BED |
| GSE185126_BA_rskd_EF_uniq.bed.gz |
5.3 Kb |
(ftp)(http) |
BED |
| GSE185126_Conserved_A673_EFpeaks_uniq.bed.gz |
142.4 Kb |
(ftp)(http) |
BED |
| GSE185126_EF_EFBs_uniq.bed.gz |
2.8 Kb |
(ftp)(http) |
BED |
| GSE185126_EF_KDBs_uniq.bed.gz |
1.6 Kb |
(ftp)(http) |
BED |
| GSE185126_EF_SBs_uniq.bed.gz |
46.2 Kb |
(ftp)(http) |
BED |
| GSE185126_EWS502log2FLIvsIgG10.bw |
173.3 Mb |
(ftp)(http) |
BW |
| GSE185126_FLI_ERG_overlaps.bed.gz |
41.5 Kb |
(ftp)(http) |
BED |
| GSE185126_FLI_ERG_overlaps_FC4_T1_IDR0.05_FDR0.05.bed.gz |
41.6 Kb |
(ftp)(http) |
BED |
| GSE185126_SKNMClog2FLIvsIgG10.bw |
218.2 Mb |
(ftp)(http) |
BW |
| GSE185126_Stable_endokd_EF_uniq.bed.gz |
41.5 Kb |
(ftp)(http) |
BED |
| GSE185126_Stable_rskd_EF_uniq.bed.gz |
42.2 Kb |
(ftp)(http) |
BED |
| GSE185126_TC71log2FLIvsIgG10.bw |
123.3 Mb |
(ftp)(http) |
BW |
| GSE185126_TTC466log2ERGvsIgG10.bw |
125.9 Mb |
(ftp)(http) |
BW |
| GSE185126_peaks_A673_FLI_fdr05_idr05_meanT1_FC4.narrowPeak.gz |
2.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE185126_peaks_EWS_502_FLI_fdr05_idr05_meanT1_FC4.narrowPeak.gz |
1.7 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE185126_peaks_SK_N_MC_FLI_fdr05_idr05_meanT1_FC4.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE185126_peaks_TC71_FLI_fdr05_idr05_meanT1_FC4.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE185126_peaks_TTC_466_ERG_fdr05_idr05_meanT1_FC4.narrowPeak.gz |
616.7 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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