|
| Status |
Public on Feb 16, 2012 |
| Title |
Chromosomal translocations are guided by the spatial organization of the genome |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
The extent to which the three-dimensional organization of the genome contributes to chromosomal translocations is an important question in cancer genomics. We now have generated a high-resolution Hi-C spatial organization map of the G1-arrested mouse pro-B cell genome and mapped translocations from target DNA double-strand breaks (DSBs) within it via high-throughput genome-wide translocation sequencing. RAG endonuclease-cleaved antigen-receptor loci are dominant translocation partners for target DSBs regardless of genomic position, reflecting high frequency DSBs at these loci and their co-localization in a fraction of cells. To directly assess spatial proximity contributions, we normalized genomic DSBs via ionizing-radiation. Under these conditions, translocations were highly enriched in cis along single chromosomes containing target DSBs and within other chromosomes and sub-chromosomal domains in a manner directly related to pre-existing spatial proximity. Our studies reveal the power of combining two high-throughput genomic methods to address long-standing questions in cancer biology.
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| |
|
| Overall design |
Hi-C interaction maps for WT and ATM -/- G1-arrested AMuLV-transformed pro-B cell lines.
|
| |
|
| Contributor(s) |
McCord RP, Zhang Y, Lajoie BR, Ho Y, Alt FW, Dekker J |
| Citation(s) |
22341456 |
| Submission date |
Feb 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Rachel Patton McCord |
| E-mail(s) |
Rachel.McCord@umassmed.edu
|
| Phone |
508-856-4377
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Gene Function and Expression
|
| Lab |
Job Dekker Lab
|
| Street address |
364 Plantation St. LRB 570M
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (7)
|
|
| Relations |
| SRA |
SRP010728 |
| BioProject |
PRJNA152237 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE35519_AMuLV-ATM-pooled-100k-allxall-ICed.txt.gz |
391.2 Mb |
(ftp)(http) |
TXT |
| GSE35519_AMuLV-ATM-pooled-10M-allxall-ICed.txt.gz |
279.3 Kb |
(ftp)(http) |
TXT |
| GSE35519_AMuLV-ATM-pooled-1M-allxall-ICed.txt.gz |
16.9 Mb |
(ftp)(http) |
TXT |
| GSE35519_AMuLV-WT-pooled-100k-allxall-ICed.txt.gz |
333.4 Mb |
(ftp)(http) |
TXT |
| GSE35519_AMuLV-WT-pooled-10M-allxall-ICed.txt.gz |
479.1 Kb |
(ftp)(http) |
TXT |
| GSE35519_AMuLV-WT-pooled-1M-allxall-ICed.txt.gz |
244.6 Kb |
(ftp)(http) |
TXT |
| GSE35519_ATM-IndivChr-ABEig.bed.gz |
143.2 Kb |
(ftp)(http) |
BED |
| GSE35519_CompartmentEigenvector_bedfiles_README.txt |
928 b |
(ftp)(http) |
TXT |
| GSE35519_ICedMatrices_README.txt |
1.2 Kb |
(ftp)(http) |
TXT |
| GSE35519_NovoOutput_README.txt |
1.2 Kb |
(ftp)(http) |
TXT |
| GSE35519_RAW.tar |
71.1 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE35519_WT-IndivChr-200kb-ABEig.bed.gz |
143.2 Kb |
(ftp)(http) |
BED |
| GSE35519_validPair_README.txt |
1.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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