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| Status |
Public on Jan 15, 2023 |
| Title |
Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Extended loop extrusion across the immunoglobulin heavy-chain (Igh) locus facilitates VH-DJH recombination in pro-B cells by aligning the VH and DJH segments for RAG-mediated cleavage. This cohesin-mediated process, resulting in global changes of the chromosome architecture in pro-B cells, depends on a 3-fold downregulation of the cohesin-release factor Wapl by Pax5-induced repression of the Wapl promoter. Here, we demonstrate that chromatin looping and VK-JK recombination at the Igk locus was insensitive to a 3-fold Wapl increase in pre-B cells. Given the equally low Wapl mRNA levels in pro-B and pre-B cells, the Wapl protein was unexpectedly expressed at a 2.2-fold higher level in pre-B cells compared to pro-B cells, which resulted in a distinct chromosomal architecture with normalized loop sizes in pre-B cells. High-resolution analysis of the Igk locus identified multiple internal loops, which likely juxtapose VK and JK elements to facilitate VK-JK recombination. The higher Wapl expression in Igm-transgenic pre-B cells prevented extended loop extrusion at the Igh locus, leading to recombination of only the 6 most 3’ proximal VH genes and to allelic exclusion of all other VH genes in pre-B cells. Hence, the different chromosomal architectures in pro-B and pre-B cells forced the Igh and Igk loci to assume distinct folding principles to undergo V gene recombination.
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| Overall design |
VDJ-Seq: Comparison of VDJ arrangements in the Igk and Igh loci. The comparison is done between wildtype (Wapl(+/+)) and mutant (Wapl(deltaP1,2/deltaP1,2) for pro-B and pre-B samples, Immature B cells (Igh locus) samples are not used for a direct comparison. Hi-C-Seq: Comparison of wildtype (Wapl(+/+) and mutant (Wapl(deltaP1,2/deltaP1,2)) samples, the Igh(B1.8hi/+) Rag2(-/-) is not used for a direct comparison. MicroC-Seq: Comparison of wildtype (Rag2(-/-)) with mutant (Igh(B1.8hi/+) Rag2(-/-)) samples. ChIP-Seq: this sample is used as phasing data for the Eigen value decomposition of Micro-C data.
Please note that the GSM6427700 records have been updated with additional processed data file on Mar 28, 2023.
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| Web link |
https://doi.org/10.1038/s41467-023-37994-9
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| Contributor(s) |
Hill L, Jaritz M, Wutz G, Tagoh H, Calderon L, Peters J, Goloborodko A, Busslinger M |
| Citation(s) |
37085514 |
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| Submission date |
Aug 02, 2022 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Mortiz M Gaidt |
| E-mail(s) |
moritz.gaidt@imp.ac.at
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| Organization name |
IMP
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| Lab |
Gaidt
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
A-1030 |
| Country |
Austria |
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| Platforms (4)
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| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (36)
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| GSM6427665 |
82653: Igk VDJ-Seq Pro-B cell Wapl(+/+) |
| GSM6427666 |
82654: Igk VDJ-Seq Pro-B cell Wapl(+/+) |
| GSM6427667 |
82655: Igk VDJ-Seq Pro-B cell Wapl(+/+) |
| GSM6427668 |
161411: Igk VDJ-Seq Pro-B cell Wapl(+/+) |
| GSM6427669 |
161412: Igk VDJ-Seq Pro-B cell Wapl(+/+) |
| GSM6427670 |
161413: Igk VDJ-Seq Pro-B cell Wapl(+/+) |
| GSM6427671 |
82656: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427672 |
82657: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427673 |
82658: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427674 |
161414: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427675 |
161415: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427676 |
161416: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427677 |
70487: Igk VDJ-Seq Pre-B cell Wapl(+/+) |
| GSM6427678 |
70488: Igk VDJ-Seq Pre-B cell Wapl(+/+) |
| GSM6427679 |
161417: Igk VDJ-Seq Pre-B cell Wapl(+/+) |
| GSM6427680 |
161418: Igk VDJ-Seq Pre-B cell Wapl(+/+) |
| GSM6427681 |
70489: Igk VDJ-Seq Pre-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427682 |
70490: Igk VDJ-Seq Pre-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427683 |
161419: Igk VDJ-Seq Pre-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427684 |
161420: Igk VDJ-Seq Pre-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427685 |
197767: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+) |
| GSM6427686 |
197768: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+) |
| GSM6427687 |
197769: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+) |
| GSM6427688 |
197770: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+) |
| GSM6427689 |
197771: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+) |
| GSM6427690 |
197772: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+) |
| GSM6427691 |
197773: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+) |
| GSM6427692 |
197774: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+) |
| GSM6427693 |
131384: HiC-Seq Pre-B cell Wapl(+/+) |
| GSM6427694 |
131385: HiC-Seq Pre-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427695 |
163563: HiC-Seq Pre-B cell Wapl(+/+) |
| GSM6427696 |
163564: HiC-Seq Pre-B cell Wapl(∆P1,2/∆P1,2) |
| GSM6427697 |
180000: HiC-Seq Pre-B cell Igh(B1.8hi/+) Rag2(-/-) |
| GSM6427698 |
180018: Micro-C Seq Pre-B cell Igh(B1.8hi/+) Rag2(-/-) |
| GSM6427699 |
180017: Micro-C Seq Pro-B cell Rag2(-/-) |
| GSM6427700 |
21476: H3K27ac ChIP-Seq Pro-B cell Rag1(Cre/Cre) |
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| Relations |
| BioProject |
PRJNA865110 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE210289_RAW.tar |
23.5 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, HIC, MCOOL, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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