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Series GSE77142 Query DataSets for GSE77142
Status Public on Jan 23, 2016
Title Activation of proto-oncogenes by disruption of chromosome neighborhoods [5C-Seq]
Organism Homo sapiens
Experiment type Other
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 5C analysis of Tal1 and LMO2 in wildtype and mutant HEK293T cells
Contributor(s) Hnisz D, Weintraub AS, Day DS, Valton A, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA
Citation(s) 26940867
Submission date Jan 22, 2016
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)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (9)
GSM2044773 Lmo2Del_rep1_miseq
GSM2044774 Lmo2Del_rep1_hiseq
GSM2044775 Lmo2Del_rep2_hiseq
This SubSeries is part of SuperSeries:
GSE68978 Activation of proto-oncogenes by disruption of chromosome neighborhoods
BioProject PRJNA309545
SRA SRP068783

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
GSE77142_8611_5CYoung-HEK239T-Lmo2Del-R2.matrix.gz 353.7 Kb (ftp)(http) MATRIX
GSE77142_8612_5CYoung-HEK239T-Tal1Del-R2.matrix.gz 371.8 Kb (ftp)(http) MATRIX
GSE77142_8613_5CYoung-HEK239T-WT-R2.matrix.gz 367.0 Kb (ftp)(http) MATRIX
GSE77142_8614_5CYoung-HEK239T-Lmo2Del.matrix.gz 431.3 Kb (ftp)(http) MATRIX
GSE77142_8614_5CYoung-HEK239T-Lmo2Del_20000_8_6343_2MbHindIIITal1_cis.matrix.gz 667.6 Kb (ftp)(http) MATRIX
GSE77142_8614_5CYoung-HEK239T-Lmo2Del_20000_8_6344_2MbHindIIILmo2_cis.matrix.gz 867.3 Kb (ftp)(http) MATRIX
GSE77142_8615_5CYoung-HEK239T-Tal1Del.matrix.gz 444.7 Kb (ftp)(http) MATRIX
GSE77142_8615_5CYoung-HEK239T-Tal1Del_20000_8_6343_2MbHindIIITal1_cis.matrix.gz 668.0 Kb (ftp)(http) MATRIX
GSE77142_8615_5CYoung-HEK239T-Tal1Del_20000_8_6344_2MbHindIIILmo2_cis.matrix.gz 886.5 Kb (ftp)(http) MATRIX
GSE77142_8616_5CYoung-HEK239T-WT.matrix.gz 438.2 Kb (ftp)(http) MATRIX
GSE77142_8616_5CYoung-HEK239T-WT_20000_8_6343_2MbHindIIITal1_cis.matrix.gz 669.1 Kb (ftp)(http) MATRIX
GSE77142_8616_5CYoung-HEK239T-WT_20000_8_6344_2MbHindIIILmo2_cis.matrix.gz 883.9 Kb (ftp)(http) MATRIX
GSE77142_8617_5CYoung-HEK239T-Lmo2Del-R1.matrix.gz 390.6 Kb (ftp)(http) MATRIX
GSE77142_8618_5CYoung-HEK239T-Tal1Del-R1.matrix.gz 400.5 Kb (ftp)(http) MATRIX
GSE77142_8619_5CYoung-HEK239T-WT-R1.matrix.gz 390.6 Kb (ftp)(http) MATRIX
GSE77142_distance-adjusted_LMO2_Lmo2Del_WT.subtract.matrix.gz 941.6 Kb (ftp)(http) MATRIX
GSE77142_distance-adjusted_LMO2_Tal1Del_WT.subtract.matrix.gz 944.4 Kb (ftp)(http) MATRIX
GSE77142_distance-adjusted_TAL1_Lmo2Del_WT.subtract.matrix.gz 728.4 Kb (ftp)(http) MATRIX
GSE77142_distance-adjusted_TAL1_Tal1Del_WT.subtract.matrix.gz 730.1 Kb (ftp)(http) MATRIX
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