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Series GSE130264 Query DataSets for GSE130264
Status Public on Sep 25, 2019
Title Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy 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
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)
GPL21626 NextSeq 550 (Mus musculus)
Samples (31)
GSM3734871 CH12F3NCdel_nonsti_input
GSM3734872 CH12F3NCdel_aCD40_IL4_TGFb_input
GSM3734873 Splenic_nonsti_input
This SubSeries is part of SuperSeries:
GSE130270 Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching
BioProject PRJNA534490
SRA SRP193756

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE130264_RAW.tar 6.3 Gb (http)(custom) TAR (of BROADPEAK, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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