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Series GSE68976 Query DataSets for GSE68976
Status Public on May 28, 2015
Title Activation of proto-oncogenes by disruption of chromosome neighborhoods [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy 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 CTCF ChIP-seq and input control in Jurkat T-ALL cells

H3K27Ac, RUNX1, and GATA3 ChIP-seq and input control in Jurkat T-ALL cells

CTCF ChIP-seq and input control in wildtype and mutant HEK293T cells
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
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 (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (10)
GSM1689151 Jurkat_CTCF_input
GSM1689152 Jurkat_CTCF_ChIP
GSM1697879 Jurkat_Runx1
This SubSeries is part of SuperSeries:
GSE68978 Activation of proto-oncogenes by disruption of chromosome neighborhoods
BioProject PRJNA284251
SRA SRP058436

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
GSE68976_RAW.tar 677.0 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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