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Series GSE112822 Query DataSets for GSE112822
Status Public on Jul 03, 2018
Title CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 2]
Organism Mus musculus
Experiment type Other
Summary RAG endonuclease initiates antibody heavy chain variable region exon assembly from V, D, and J segments within a chromosomal V(D)J recombination center (RC) by cleaving between paired gene segments and flanking recombination signal sequences (RSSs). The IGCR1 control region promotes DJH intermediate formation by isolating Ds, JHs, and RC from upstream VHs in a chromatin loop anchored by CTCF-binding elements ("CBEs"). How VHs access the DJHRC for VH to DJH rearrangement was unknown. We report that CBEs immediately downstream of frequently rearranged VH-RSSs increase recombination potential of their associated VH far beyond that provided by RSSs alone. This CBE activity becomes particularly striking upon IGCR1 inactivation, which allows RAG, likely via loop extrusion, to linearly scan chromatin far upstream. VH-associated CBEs stabilize interactions of D-proximal VHs first encountered by the DJHRC during linear RAG scanning and, thereby, promote dominant rearrangement of these VHs by an unanticipated chromatin accessibility-enhancing CBE function.
Overall design We performed HTGTS on v-Abl kinase transformed pro-B cell lines using a JH4 coding end primer as bait to examine the relative utilization of different VH segements in WT and mutant lines. All lines analyzed were derived from a parental WT line that harbors a non-productive VDJH rearrangement involving a distal VHJ558 (VH1-2P) which deletes the entire proximal VH domain on one allele and is inert for V(D)J recombination. The other allele harbors a DHFL16.1 to JH4 rearrangement (DJH allele) and can actively undergo VH to DJH recombination upon G1 arrest induced by STI-571 treatment. The DJ allele was genetically manipulated to derive the various mutants.
Contributor(s) Jain S, Ba Z, Zhang Y, Dai H, Alt FW
Citation(s) 29804837
Submission date Apr 06, 2018
Last update date Jan 27, 2019
Contact name Suvi Jain
Organization name Boston Children's Hospital
Department Molecular Medicine
Lab Frederick W. Alt
Street address 300 LONGWOOD AVE
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (36)
GSM3084364 DJ_WT_rep1
GSM3084365 DJ_WT_rep2
GSM3084366 DJ_WT_rep3
This SubSeries is part of SuperSeries:
GSE113023 CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning
BioProject PRJNA449088
SRA SRP137888

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Supplementary file Size Download File type/resource
GSE112822_RAW.tar 225.8 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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