|
| Status |
Public on Aug 15, 2022 |
| Title |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (RNA-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
|
| 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.
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| |
|
| Overall design |
RNA-sequencing of A673 and TC71 Ewing sarcoma cells containing EWS/FLI or depleted of EWS/FLI using RNAi
|
| |
|
| 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 (4)
|
|
| This SubSeries is part of SuperSeries: |
| GSE185132 |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma |
|
| Relations |
| Reanalysis of |
GSM4885656 |
| Reanalysis of |
GSM4885661 |
| Reanalysis of |
GSM4885657 |
| Reanalysis of |
GSM4885662 |
| Reanalysis of |
GSM4885658 |
| Reanalysis of |
GSM4885663 |
| BioProject |
PRJNA767693 |
| SRA |
SRP339581 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE185130_A673_RNAseq_iEF_197.bw |
64.4 Mb |
(ftp)(http) |
BW |
| GSE185130_A673_RNAseq_iEF_714.bw |
53.2 Mb |
(ftp)(http) |
BW |
| GSE185130_A673_RNAseq_iEFwtEF714vsiEFempty197.complete.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| GSE185130_A673_RNAseq_iLuc_197.bw |
51.1 Mb |
(ftp)(http) |
BW |
| GSE185130_A673_RNAseq_iLucempty197vsiEFempty197.complete.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| GSE185130_AllData_200715_Lessnick_Iftekhar_GSL-IS-1690_Results.xlsx |
5.8 Mb |
(ftp)(http) |
XLSX |
| GSE185130_EWSFLI_directdowninA673_iLuc197vsiEF197.grp.txt.gz |
1.5 Kb |
(ftp)(http) |
TXT |
| GSE185130_EWSFLI_directupin_A673_iLuc197vsiEF197.grp.txt.gz |
3.0 Kb |
(ftp)(http) |
TXT |
| GSE185130_TC71_EndovsKD_DEG_RO.txt.gz |
136.1 Kb |
(ftp)(http) |
TXT |
| GSE185130_TC71_iEF_RNAseq.bw |
247.1 Mb |
(ftp)(http) |
BW |
| GSE185130_TC71_iLuc_RNAseq.bw |
220.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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