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Series GSE68975 Query DataSets for GSE68975
Status Public on May 28, 2015
Title Activation of proto-oncogenes by disruption of chromosome neighborhoods [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Mutations such as gene fusion, translocation and focal amplification are a frequent cause of proto-oncogene activation during tumorigenesis, but such mutations do not explain all cases of proto-oncogene activation. Here we show that disruption of local chromosome conformation can also activate proto-oncogenes in human cells. We mapped chromosome structures in T-cell acute lymphoblastic leukemia (T-ALL), and found that active oncogenes and silent proto-oncogenes generally occur within insulated neighborhoods formed by the looping of two interacting CTCF sites co-occupied by cohesin. Recurrent microdeletions frequently overlap neighborhood boundary sites in T-ALL genomes, and we demonstrate that site-specific perturbation of loop boundaries is sufficient to activate the respective proto-oncogenes in non-malignant cells. We found somatic genomic rearrangements affecting loop boundaries in many cancers. These results suggest that chromosome structural organization is fundamental to identify functional somatic alterations in cancer genomes.
 
Overall design Paired-end 80x80 Poly-A RNA-seq in Jurkat T-ALL
 
Contributor(s) Hnisz D, Weintraub AS, Fan ZP, Abraham BJ, Sigova AA, Reddy J, Lee TI, Young RA
Citation(s) 26940867
Submission date May 18, 2015
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (1)
GSM1689150 Jurkat_polyA_RNA-Seq
This SubSeries is part of SuperSeries:
GSE68978 Activation of proto-oncogenes by disruption of chromosome neighborhoods
Relations
BioProject PRJNA284252
SRA SRP058435

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Supplementary file Size Download File type/resource
GSE68975_RAW.tar 11.7 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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