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Series GSE130265 Query DataSets for GSE130265
Status Public on Sep 25, 2019
Title Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [CSR-HTGTS-Seq]
Organism Mus musculus
Experiment type Genome variation profiling by high throughput sequencing
Summary In a B lymphocyte immunoglobulin heavy chain locus (IgH), a developmentally assembled V(D)J exon encoding an antibody variable region lies upstream of exons encoding a  constant region (C), allowing generation of IgH chain transcripts and IgM-class antibodies1. Mouse IgH class switch recombination (CSR) replaces Cwith one of 6 sets of constant region exons (CHs) that lie 100-200kb downstream1. Each CH is flanked upstream by a promoter, non-coding I-exon, and long repetitive switch (S) region1,2. Cytokines/activators induce specific I-promoter transcription and activation-induced cytidine deaminase (AID)2,3. AID is transcriptionally-targeted to initiate DNA breaks in S and activated downstream acceptor S regions, which are joined in deletional orientation to complete CSR4,5. 3’IgH regulatory region (3’IgHRR) enhancers control upstream I promoters and, thereby, CSR via linear competition involving I promoter/3’IgHRR interactions6-11. Here, we report that synapsis of regulatory elements, S regions and DSBs for CSR is achieved by chromatin loop extrusion. In naive B cells, 3’IgHRR enhancers and adjacent 3’IgH CTCF-binding elements (CBEs) interact via loop extrusion with the upstream Igh intronic enhancer (iE)/S locale to generate dynamic 200kb 3’Igh basal loop. In CSR-activated B cells, induced transcription from I-promoters within this basal loop generates dynamic sub-loops that directionally align S and target S regions near the 3’IgHRR for CSR. In CH12F3 B lymphoma cells, inactivation of the constitutively active I-promoter abrogates looping and CSR to S, while activating transcription, looping, and CSR to upstream S regions. CBEs inserted upstream of I in convergent orientation with 3’IgH CBEs generate sub-loops that activate inversional S CSR. In I-promoter-deleted CH12F3 cells, this ectopic CBE-based sub-loop inactivates upstream S region CSR, while transcriptionally activating non-S region sequences adjacent to the inserted CBEs for S synapsis and CSR. Together, our findings implicate chromatin loop extrusion in the “unprecedented mechanism”5 by which Igh organization in cis promotes orientation-specific CSR DSB joining.
 
Overall design We performed CSR-HTGTS-Seq, 3C-HTGTS, GRO-Seq and ChIP-Seq in mature splenic B cells with different stimulation and different mutants of CH12F3 cells to study roles of cohesin-mediated chromatin loop extrusion in IgH class switch recombination.
 
Contributor(s) Zhang X, Alt FW
Citation(s) 31666703
Submission date Apr 24, 2019
Last update date Nov 15, 2019
Contact name Frederick W Alt
E-mail(s) jianqiao.hu@childrens.harvard.edu
Organization name Boston Children's Hospital
Department PCMM
Lab Alt
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (21)
GSM3734883 CH12F3NCD 1
GSM3734884 CH12F3NCD 2
GSM3734885 CH12F3NCD 3
This SubSeries is part of SuperSeries:
GSE130270 Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching
Relations
BioProject PRJNA534492
SRA SRP193757

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
GSE130265_RAW.tar 3.3 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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