Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells

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. 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.