Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Miswired enhancer logic drives translocation positive rhabdomyosarcoma

ABSTRACT: Miswired enhancer logic drives translocation positive rhabdomyosarcoma

PROVIDER: PRJNA563682 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10062460.fastq.gz	Fastqsanger.gz
	SRR10062461.fastq.gz	Fastqsanger.gz
	SRR10062462.fastq.gz	Fastqsanger.gz
	SRR10062463.fastq.gz	Fastqsanger.gz
	SRR10062464.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Miswired enhancer logic drives translocation positive rhabdomyosarcoma

Project description:Core regularity transcription factors (CR TFs) define cell identity and lineage through an exquisitely precise and logical order during embryogenesis and development. These CR TFs regulated one another in three-dimensional space via distal enhancers that serve as logic gates embedded in their TF recognition sequences. Aberrant chromatin organization resulting in miswired circuitry of enhancer logic is a newly recognized feature in many cancers. Here, we report that PAX3-FOXO1 expression is driven by a translocated FOXO1 distal super enhancer (SE). ChIP-seq in tumors bearing rare PAX translocations implicate enhancer miswiring is a pervasive feature across all FP-RMS tumors. Therefore, our data reveal a mechanism of a translocated hijacked enhancer which disrupts the normal CR TF logic during skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an infinite loop logic that makes rhabdomyosarcoma cells unable to exit the undifferentiated proliferating stage.

2019-12-25 | GSE136799 | GEO

Transcription profiling of human Rhabdomyosarcoma biopsy samples (15 embryonal RMS, 10 translocation-positive alveolar RMS and 5 translocation-negative alveolar RMS)

Project description:We measured the expression profiles of a series of 30 Rhabdomyosarcoma biopsy samples (15 embryonal RMS, 10 translocation-positive alveolar RMS and 5 translocation-negative alveolar RMS). Expression data was used for unsupervised hierarchical clustering as well as supervised analysis to find gene expression signatures characteristic for the different histological RMS subgroups.

2004-06-30 | E-MEXP-121 | biostudies-arrayexpress

Multiplex enhancer-reporter assays uncover unsophisticated p53 enhancer logic

Project description:Multiplex enhancer-reporter assays uncover unsophisticated p53 enhancer logic

| PRJNA308235 | ENA

Expression Profiling of human Fusion-Positive and Fusion-Negative Rhabdomyosarcoma

Project description:Genome-wide gene expression in 33 fusion-positive and 25 fusion-negative rhabdomyosarcoma cases was studied using GeneChip Human Genome U133 Plus2 (Affymetrix) Fusion-positive versus fusion-negative rhabdomyosarcoma tumors

2016-06-01 | E-GEOD-66533 | biostudies-arrayexpress

Genome-wide map of PAX3-FKHR binding sites in rhabdomyosarcoma

Project description:We report the genome-wide maps of PAX3-FKHR binding sites. Chromatin immunoprecipitation was performed against PAX3-FKHR positive (Rh4) and PAX3-FKHR negative (RD) rhabdomyosarcoma cells with a monoclonal antibody (pFM2) specific for the fusion region of PAX3-FKHR. We obtained 4 million sequence tags for both input and ChIP DNA that aligned to the human genome. We identified 1,463 binding sites from ChIP-seq of Rh4 cells, none of which appeared from ChIP-seq of fusion negative RD cells. The PAX3-FKHR binding sites were found to associate with 1,072 genes in RMS cells. The data shows that PAX3-FKHR binds to the same sites as PAX3, at the enhancers for MYF5, FGFR4, and the MYOD core enhancer previously shown to be regulated by PAX3. Moreover, our dataset has the precision for rapid identification and validation of novel and specific sequences required for the enhancer activity of MYOD and FGFR4. The genome wide analysis reveals that the PAX3-FKHR sites are: 1) mostly distal to transcription start sites; 2) conserved; 3) enriched for PAX3 motifs; and 4) strongly associated with genes over-expressed in PAX3-FKHR positive RMS cells and tumors. There is little evidence in our dataset for PAX3-FKHR binding at the promoters. In one instance, we show two intronic enhancer elements for MET, rather than at the previously described promoter. The genome-wide analysis further illustrates a strong association between PAX3 and E-box motifs in these binding sites, suggestive of a common co-regulation for many target genes. The map of PAX3-FKHR binding sites provides new links for PAX3 and PAX3-FKHR functions and new targets for RMS therapy. Examination of PAX3-FKHR binding sites in translocation-positive rhabdomyosarcoma cells via ChIP-seq with an antibody specific for the fusion protein.

2010-08-17 | E-GEOD-19063 | biostudies-arrayexpress

Defining the interactome of CHD4 in fusion-positive rhabdomyosarcoma

Project description:The goal of this study was to explore in detail how the chromatin remodeler and NuRD subunit CHD4 controls the oncogenic signature of the tumor driver and fusion protein PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. To this aim, we defined the interactome of CHD4 by LC-MS, identified its location in the genome by ChIP-seq, assessed its influence on DNA accessibility by DNase I hypersensitivity assays, and determined its target genes by RNA-seq.

2020-08-11 | PXD015231 | Pride

Compatibility logic of human enhancer and promoter sequences

Project description:Compatibility logic of human enhancer and promoter sequences

| PRJNA764659 | ENA

CHD4 regulates super-enhancer accessibility in fusion-positive rhabdomyosarcoma and is essential for tumor growth

Project description:CHD4 regulates super-enhancer accessibility in fusion-positive rhabdomyosarcoma and is essential for tumor growth

| PRJNA588286 | ENA

Expression Profiling of human Fusion-Positive and Fusion-Negative Rhabdomyosarcoma

Project description:Genome-wide gene expression in 33 fusion-positive and 25 fusion-negative rhabdomyosarcoma cases was studied using GeneChip Human Genome U133 Plus2 (Affymetrix)

2016-06-01 | GSE66533 | GEO

Longitudinal biopsies of fusion-positive rhabdomyosarcoma orthotopic xenografts

Project description:Longitudinal biopsies of fusion-positive rhabdomyosarcoma orthotopic xenografts

| PRJNA1003123 | ENA