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Series GSE99195 Query DataSets for GSE99195
Status Public on Jun 28, 2017
Title Genome Organization Drives Chromosome Fragility [ChIP-seq]
Organisms Mus musculus; Mus spretus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In this study, we show that evolutionarily conserved chromosome loop anchors bound by CTCF and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy concomitantly rewire DNA cleavage sites to novel contact domain boundaries. While transcription and replication coupled genomic rearrangements have been well documented, we demonstrate that DSBs at loop anchors are transcription-, replication-, and cell type- independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in acute leukemias and prostate cancers. Thus, loop anchors serve as preferred and promiscuous fragile sites that generate DSBs and chromosomal rearrangements.
Overall design ChIP-seq profile in Activated and resting B cells, MEFs, pre-B cells, T cells, and Neurons
Contributor(s) Canela A, Maman Y, Jung S, Wong N, Day A, Callen E, Jung S, Kieffer-Kwon K, Pekowska A, Zhang H, Mckinnon PJ, Aplan PD, Pommier Y, Lieberman Aiden E, Casellas R, Nussenzweig A
Citation(s) 28735753
Submission date May 23, 2017
Last update date Jul 25, 2021
Contact name Yaakov Maman
Organization name Bar-Ilan University
Department Azrieli Faculty of Medicine
Lab Genome Instability & Cancer
Street address Henrietta Szold 8
City Safed
ZIP/Postal code 1311502
Country Israel
Platforms (2)
GPL21626 NextSeq 550 (Mus musculus)
GPL23505 NextSeq 550 (Mus spretus)
Samples (18)
GSM2635592 ChIP_seq_CTCF_aB
GSM2635593 ChIP_seq_CTCF_MEF
GSM2635594 ChIP_seq_CTCF_rB
This SubSeries is part of SuperSeries:
GSE99197 Genome Organization Drives Chromosome Fragility
BioProject PRJNA387544
SRA SRP107840

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
GSE99195_RAW.tar 4.8 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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