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Series GSE73007 Query DataSets for GSE73007
Status Public on Sep 15, 2015
Title On-target and Off-target Activities of RAG Are Restricted by Topological Chromatin Domains
Organism Mus musculus
Experiment type Other
Summary RAG initiates V(D)J recombination in developing lymphocytes by generating "on-target" DNA double-stranded breaks at bona fide recombination signal sequence (RSS) pairs. We now employ RAG-generated DNA breaks in endogenous or ectopically-inserted RSS pairs as bait to identify huge numbers of RAG "off-target" sites. These off-target DNA breaks occur across convergent CTCF-binding element (CBE)-flanked loop domains containing the bait RSS pairs. Such off-target cleavage occurs at the simple CAC motif that defines the RSS cleavage-site and shows orientation-dependence best explained by a two-dimensional tracking mechanism. Deletion of the CBE-based IGCR1 IgH regulatory element disrupts antibody IgH recombination domains and, correspondingly, alters distributions of RAG on- and off-targets across the IgH locus. RAG off-targets frequently involved in chromosomal translocations occur in convergent RSS pairs at enhancer regions within a loop. Our findings reveal how RAG is developmentally focused and re-focused in lymphocytes and implicate mechanisms by which chromatin domains harness biological processes within them.
Overall design We performed high-throughput genome-wide translocation sequencing (HTGTS) in progenitor B cells or cell lines to study signatures of RAG on and off-targeting activity using RAG-generated breaks in endogenous or ectopically-inserted paired bona fide RSSs as bait. Sequenceing was dong by Illumina Miseq.
Contributor(s) Alt FW, Hu J, Zhang Y
Citation(s) 26593423
Submission date Sep 14, 2015
Last update date May 15, 2019
Contact name Jiazhi Hu
Organization name Children's Hospital Boston
Department PCMM
Lab Frederick Alt
Street address 300 Longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (40)
GSM1880614 IgH-AB-rep1
GSM1880615 IgH-AB-rep2
GSM1880616 IgH-AB-rep3
BioProject PRJNA295978
SRA SRP063873

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE73007_IgH-AB-dIGCR1-pooled.txt.gz 20.9 Mb (ftp)(http) TXT
GSE73007_IgH-AB-pooled.txt.gz 1.2 Mb (ftp)(http) TXT
GSE73007_RAW.tar 63.8 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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