GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE69439 Query DataSets for GSE69439
Status Public on Apr 17, 2017
Title Regulatory landscape fusion in rhabdomyosarcoma by interactions between the PAX3 promoter and FOXO1 regulatory elements
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Results: Using a combination of 4C-seq datasets, we were able to model the three-dimensional organisation of the translocated chromosome in a PAX3:FOXO1 fusion-positive alveolar rhabdomyosarcoma cell line. We show that PAX3 and FOXO1 regulatory landscapes fuse into a novel TAD, allowing the PAX3 promoter to interact ectopically with FOXO1 sequences with potential enhancer function. The borders of this novel TAD correspond to the original 5'- and 3'- borders of the PAX3 and FOXO1 TADs, respectively, suggesting that TAD organisation precedes the formation of regulatory long-range interactions.

Conclusions: Our results suggest that the chromosomal translocation that leads to ARMS development generates a novel TAD that favours ectopic PAX3:FOXO1 oncogene activation in non-PAX3 territories, which may be an essential step in the tumorigenic process, as expression in a particular cell type, the often elusive cell-of-origin, may be required for disease development.
Overall design 4C-seq samples for FoxO1 and Pax3 gene promoters in E9.5 whole mouse embryos, as well as for the PAX3 promoter and several ECRs and CTCF binding sites present at the PAX3:FOXO1 locus in the patient-derived alveolar rhabdomyosarcoma (ARMS) cell line RMS.
Contributor(s) Vicente-García C, Villarejo-Balcells B, Irastorza-Azcárate I, Naranjo S, Acemel RD, Tena JJ, Rigby PW, Devos DP, Gómez-Skarmeta JL, Carvajal JJ
Citation(s) 28615069
Submission date Jun 01, 2015
Last update date May 15, 2019
Contact name Juan J. Tena
Organization name CABD/CSIC
Street address Univ. Pablo Olavide, Ctra. Utrera km1
City Sevilla
ZIP/Postal code 41013
Country Spain
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (11)
GSM1701245 4C-Seq for FoxO1 promoter in E9.5 mouse embryos
GSM1701246 4C-Seq for Pax3 promoter in E9.5 mouse embryos
GSM1701247 4C-Seq for PAX3 promoter in patient-derived RMS cells
BioProject PRJNA285501
SRA SRP058950

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69439_RAW.tar 20.1 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap