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GEO help: Mouse over screen elements for information. |
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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
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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 Cwith 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.
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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.
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Contributor(s) |
Zhang X, Alt FW |
Citation(s) |
31666703 |
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Submission date |
Apr 24, 2019 |
Last update date |
Nov 15, 2019 |
Contact name |
Frederick W Alt |
E-mail(s) |
jianqiao.hu@childrens.harvard.edu
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Organization name |
Boston Children's Hospital
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Department |
PCMM
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Lab |
Alt
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Street address |
1 Blackfan Circle
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
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Platforms (1) |
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Samples (21)
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This SubSeries is part of SuperSeries: |
GSE130270 |
Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching |
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Relations |
BioProject |
PRJNA534492 |
SRA |
SRP193757 |
Supplementary file |
Size |
Download |
File type/resource |
GSE130265_RAW.tar |
3.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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