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Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [END-seq]

ABSTRACT: Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [END-seq]

PROVIDER: PRJNA590463 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10493669.fastq.gz	Fastqsanger.gz
	SRR10493670.fastq.gz	Fastqsanger.gz
	SRR10493671.fastq.gz	Fastqsanger.gz
	SRR10493672.fastq.gz	Fastqsanger.gz
	SRR10493673.fastq.gz	Fastqsanger.gz

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Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire

Project description:Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire

| PRJNA590489 | ENA

Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [HTGTS]

Project description:Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [HTGTS]

| PRJNA590491 | ENA

Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [ChIP-seq]

Project description:Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [ChIP-seq]

| PRJNA590470 | ENA

Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [END-seq]

Project description:During V(D)J recombination RAG proteins introduce DNA double strand breaks (DSBs) adjacent to conserved recombination signal sequences (RSS) that contain either 12- or 23-nucleotide spacer regions. Coordinated cleavage following the “12/23” rule predicts that DSBs at variable (V) gene segments should not exceed the level of breakage at joining (J) segments, thereby ensuring that V regions do not engage in undesirable recombination events with one another. Here we report abundant RAG dependent DSBs at a multitude of V gene segments within the Ig locus independent of V-J rearrangement. We discover that a large fraction of V gene segments are flanked not only by a bone-fide 12 spacer, but also an overlapping, 23 spacer flipped RSS. These compatible pairs of RSS mediate recombination and deletion inside the V cluster even in the complete absence of J gene segments, and support a novel recombination center (RC) independent of the conventional J-centered RC. We propose a model that explains V gene segment usage by taking into account not only the probability of V-to-J rearrangement but also the surprisingly frequent, evolutionarily conserved intra-V cluster recombination events. These findings shed light on the diverse molecular strategies that shape the primary antigen receptor repertoires.

2020-01-01 | GSE140635 | GEO

Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [HTGTS]

2020-01-01 | GSE140672 | GEO

Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [ChIP-seq]

2020-01-01 | GSE140655 | GEO

Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-01-01 | GSE140677 | GEO

Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire.

Project description:During V(D)J recombination, RAG proteins introduce DNA double-strand breaks (DSBs) at recombination signal sequences (RSSs) that contain either 12- or 23-nt spacer regions. Coordinated 12/23 cleavage predicts that DSBs at variable (V) gene segments should equal the level of breakage at joining (J) segments. Contrary to this, here we report abundant RAG-dependent DSBs at multiple Vκ gene segments independent of V-J rearrangement. We find that a large fraction of Vκ gene segments are flanked not only by a bone-fide 12 spacer but also an overlapping, 23-spacer flipped RSS. These compatible pairs of RSSs mediate recombination and deletion inside the Vκ cluster even in the complete absence of Jκ gene segments and support a V(D)J recombination center (RC) independent of the conventional Jκ-centered RC. We propose an improved model of Vκ-Jκ repertoire formation by incorporating these surprisingly frequent, evolutionarily conserved intra-Vκ cluster recombination events.

| S-EPMC8214342 | biostudies-literature

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination

Project description:Background: V(D)J recombination is an essential process for the generation of diverse antigen receptor (AgR) repertoires. In B cells, immunoglobulin kappa (Igk) light chain locus recombination follows recombination of the immunoglobulin heavy chain (Igh) locus. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. In conjunction with genome-wide datasets for several epigenetic features, we showed that two active chromatin states, located at the recombination signal sequences (RSS) of VH genes, are highly predictive of recombination. The contribution of chromatin features to Vk gene choice in recombination remains poorly understood. Results: We adapted the VDJ-seq assay to profile the Igk VkJk repertoire, and obtained a comprehensive readout of highly variable Vk gene usage in mouse bone marrow pre-B cells. We identified PU.1 binding at the RSS as highly predictive of whether a gene will actively recombine or not. Prediction of the frequency of recombination was more dependent on H3K4 methylation and IKAROS binding. Conclusions: Epigenetic features within the Vk region are able to explain much of the variation in Vk gene usage. Whilst PU.1 binding at the RSS appears to play a binary, all-or-nothing role, priming Vk genes for recombination, the frequency with which these genes recombine is shaped by the presence and enrichment of a number of other epigenetic features. In contrast to the Igh locus, the epigenetic landscape of the promoter as well as the RSS is predictive of Vk gene recombination.

2017-11-03 | GSE101606 | GEO

Analysis of gene expression in Ig-lambda/kappa positive bone marrow wild type/TAK1-/- B cell

Project description:The activation signaling of transcription factor nuclear factor-kB (NF-kB) plays central role for immune system. One of key kinase mediating this pathway is TAK1 in adaptive and innate immunity. However, role of TAK1 in bone marrow B cell is still unclear. To know effects of TAK1-deletion, the gene expression of Ig-lambda/kappa positive cells were analyzed in comparison of wild type with TAK1-deficient bone marrow B cells.

2015-10-22 | GSE74248 | GEO

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