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| Status |
Public on Dec 04, 2018 |
| Title |
Genome-wide chromatin analysis of Ewing sarcoma (ChIP-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
As the second most common malignant bone tumor in children and adolescents, Ewing sarcoma is initiated and exacerbated by a chimeric oncoprotein, most commonly, EWS-FLI1. In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. Through integrative analysis, we identify MEIS1 as a super-enhancer-driven oncogene, which co-operates with EWS-FLI1 in transcriptional regulation, and plays a key pro-survival role in Ewing sarcoma. Moreover, APCDD1, another super-enhancer-associated gene, acting as a downstream target of both MEIS1 and EWS-FLI1, is also characterized as a novel tumor-promoting factor in this malignancy. These data delineate super-enhancer-mediated transcriptional deregulation in Ewing sarcoma, and uncover numerous candidate oncogenes which can be exploited for further understanding of the molecular pathogenesis for this disease.
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| Overall design |
ChIP-seq for MEIS1 in A673 Ewing sarcoma cells
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| Contributor(s) |
Lin L, Lin D |
| Citation(s) |
30496486 |
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| Submission date |
Jan 23, 2018 |
| Last update date |
Dec 23, 2018 |
| Contact name |
Lehang Lin |
| E-mail(s) |
linlh7@mail2.sysu.edu.cn
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| Organization name |
Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University
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| Street address |
107, West Yanjiang Road
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| City |
Guangzhou |
| ZIP/Postal code |
510120 |
| Country |
China |
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| Platforms (1) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA431168 |
| SRA |
SRP131113 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE109477_RAW.tar |
84.5 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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