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Series GSE130224 Query DataSets for GSE130224
Status Public on Aug 19, 2019
Title The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Genome variation profiling by high throughput sequencing
Summary RAG endonuclease initiates IgH locus (Igh) V(D)J assembly in progenitor (pro)-B cells by joining Ds to JHs, before joining upstream VHs to DJH intermediates. In mouse pro-B cells, the CTCF-binding element (CBE)-anchored chromatin loop domain at the 3’end of Igh contains an internal sub-domain spanning the 5’CBE anchor (IGCR1), the DHs, and a RAG-bound recombination center (RC). The RC comprises JH-proximal D (DQ52), 4 JHs, and the intronic enhancer (“iEmu”). Robust RAG cleavage is restricted to paired V(D)J segments flanked by complementary recombination signal sequences (12RSSs and 23RSSs). Ds are flanked downstream and upstream by 12RSSs that, respectively, mediate deletional joining with convergently-oriented JH-23RSSs and VH-23RSSs. Despite 12/23 compatibility, inversional D to JH joining via upstream D-12RSSs is rare. Plasmid-based assays attributed lack of inversional D to JH joining to sequence-based preference for downstream D-12RSSs, as opposed to putative linear scanning mechanisms. Given recent findings that RAG linearly scans convergent CBE-anchored chromatin loops, potentially formed by cohesin-mediated loop extrusion, we revisited a scanning role. Here, we report that JH-23RSS chromosomal orientation programs RC-bound RAG to linearly scan upstream chromatin in the 3’Igh sub-domain for convergently-oriented D-12RSSs and, thereby, to mediate deletional joining of all Ds, except RC-based DQ52 that joins by a diffusion-related mechanism. In a DQ52-based RC, formed in the absence of JHs, RAG bound by the downstream DQ52-RSS scans the downstream constant region exon-containing 3’Igh sub-domain in which scanning can be impeded by targeted nuclease-dead Cas9 (dCas9) binding, by transcription through repetitive Igh switch sequences, and by the 3’Igh CBE-based loop anchor. Notably, each scanning impediment focally increases RAG activity on potential substrate sequences within the impeded region. High resolution mapping of RC chromatin interactions reveals that such focal RAG targeting is associated with corresponding impediments to the loop extrusion process that drives chromatin past RC-bound RAG.
 
Overall design We performed HTGTS V(D)J-seq, 3C-HTGTS, GRO-Seq, ChIP-Seq and Hi-C in v-Abl transformed pro-B cells to study roles of chromatin loop extrusion-mediated RAG scanning in IgH V(D)J recombination.
 
Citation(s) 31511698
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AI020047 Mechanisms That Control Antigen Receptor Variable Region Exon Assembly CHILDREN'S HOSPITAL Frederick W. Alt
Submission date Apr 23, 2019
Last update date Oct 02, 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 (3)
GPL16417 Illumina MiSeq (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (133)
GSM3733923 Rad21_dCas9Control_Input
GSM3733924 Rad21_dCas9Block_Input
GSM3733925 Rad21_dCas9Control_rep1
This SuperSeries is composed of the following SubSeries:
GSE130213 The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [ChIP-Seq]
GSE130214 The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [3C-HTGTS]
GSE130215 The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [GRO-Seq]
Relations
BioProject PRJNA534311

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
GSE130224_RAW.tar 89.7 Gb (http)(custom) TAR (of BED, BEDGRAPH, BEDPE, BW, HIC, TXT)
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