An enhancer in the middle of the Igκ locus orchestrates nuclear architecture to generate a diverse antigen receptor repertoire
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA496404 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8053840.fastq.gz | Fastqsanger.gz | |||
| SRR8053841.fastq.gz | Fastqsanger.gz | |||
| SRR8053842.fastq.gz | Fastqsanger.gz | |||
| SRR8053843.fastq.gz | Fastqsanger.gz | |||
| SRR8053844.fastq.gz | Fastqsanger.gz |
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Project description:Purpose:The goal of this study is to assess transcriptome profile in the absence of a potent enhancer located in the V gene region of the Igκ locus in cell lines and mice Methods: RNAseq from CD19+ cells from B6.RAG1-/- and E88-/-.RAG1-/- mice. RNAseq from 445.3, wild-type (WT) and E88-/-, pro-B cell lines
2018-11-15 | GSE121224 | GEO
Project description:Although much research has been done to understand how rearrangement of the Igκ locus is regulated during B-cell development, very little is known about the way the variable (V) segments themselves are selected. Using B6/Cast hybrid pre-B cell clones, we show that a limited number of V segments on each allele is stochastically activated as characterized by the appearance of ncRNA and histone modifications. The activation states are clonally distinct, stable across cell division and developmentally important in directing the Ig repertoire upon differentiation. By employing a new approach of allelic ATAC-seq we demonstrate that the Igκ V alleles have differential chromatin accessibility, which may serve as the underlying basis of clonal maintenance at this locus, as well as other instances of monoallelic expression throughout the genome. These findings highlight a new level of immune-system regulation that appears to be geared at optimizing gene diversity.
2017-04-01 | GSE97148 | GEO
Project description:The genome is organized into topologically associated domains (TADs) that enclose smaller subTADs. Here, we identify and characterize an enhancer that is located in the middle of the V gene region of the immunoglobulin kappa light chain (Igκ) locus that becomes active preceding the stage at which this locus undergoes V(D)J recombination. This enhancer is a hub of long-range chromatin interactions connecting subTADs in the V gene region with the recombination center at the J genes. Deletion of this element results in a highly altered long-range chromatin interaction pattern across the locus and, importantly, affects individual V gene utilization locus-wide. These results indicate the existence of an enhancer-dependent framework in the Igκ locus and further suggest that the composition of the diverse antibody repertoire is regulated in a subTAD-specific manner. This enhancer thus plays a structural role in orchestrating the proper folding of the Igκ locus in preparation for V(D)J recombination.
| S-EPMC6610861 | biostudies-literature
Project description:Dynamic genome folding plays a crucial role in cellular functions, including V(D)J recombination at the immunoglobulin kappa (Igκ) locus for antibody generation. This process involves frequent recombination between Jκ and Vκ gene segments over a 3.2 Mb region in both deletional and inversional orientations. While loop extrusion and diffusion are thought to facilitate Igκ recombination, their cooperative mechanisms remain unclear. Our study demonstrates CTCF as a key regulator coupling loop extrusion and diffusion to enhance Vκ recombination in both orientations across large genomic distances. We show that CTCF's N-terminus promotes long-range loop extrusion important for distal Vκ usage by stabilizing cohesin against Wapl release. Furthermore, CTCF's loop barrier function is essential for inversional Vκ usage via enabling diffusion. In CTCF N-terminus mutants, defects in inversional Vκ joining were not corrected by Wapl depletion alone but improved with targeted dCas9 blockade mimicking the CTCF barrier. These findings reveal that CTCF regulates immune diversity via diverse mechanisms and underscore its versatility in gene regulation.
2025-11-20 | PXD058006 | Pride
Project description:The generation of a diverse and self-tolerant B cell repertoire is essential for adaptive immunity and is achieved through V(D)J recombination. In mice, Igκ is the dominant light chain, whereas Igλ rearrangement typically occurs in response to nonproductive or autoreactive Igκ recombination, a process termed receptor editing. Recombination at the RS element deletes the Igκ constant exon, silencing the locus and enabling Igλ expression. However, the epigenetic regulatory framework that orchestrates and governs receptor editing remains poorly defined. Here, we identify a CTCF-binding insulator element (CBE) within the 3′ Igκ super-enhancer (3′-SEκ) that regulates receptor editing and directs the κ-to-λ switch required for Igλ⁺ B-cell development. Mechanistically, loss of this CBE activates an insulated enhancer within the 3′-SEκ, causing aberrant Vκ rearrangements and altered chromatin interactions through disrupted loop extrusion dynamics. Notably, loss of this CBE in mice leads to increased autoantibody production by ten weeks of age, demonstrating that CBE-mediated chromatin architecture shapes B cell fate by constraining autoreactive potential. Collectively, our findings define a novel CTCF-dependent cis- regulatory insulation checkpoint that connects chromatin loop extrusion to antigen- driven receptor editing, thereby enforcing B-cell tolerance.
2026-01-15 | GSE313431 | GEO
Project description:Although much has been done to understand how rearrangement of the Igκ locus is regulated during B-cell development, little is known about the way the variable (V) segments themselves are selected. Here we show, using B6/Cast hybrid pre-B-cell clones, that a limited number of V segments on each allele is stochastically activated as characterized by the appearance of non-coding RNA and histone modifications. The activation states are clonally distinct, stable across cell division and developmentally important in directing the Ig repertoire upon differentiation. Using a new approach of allelic ATAC-seq, we demonstrate that the Igκ V alleles have differential chromatin accessibility, which may serve as the underlying basis of clonal maintenance at this locus, as well as other instances of monoallelic expression throughout the genome. These findings highlight a new level of immune system regulation that optimizes gene diversity.
| S-EPMC5459994 | biostudies-literature
Project description:Conditional knock-out (KO) of Polycomb Group (PcG) protein YY1 results in pro-B cell arrest and reduced immunoglobulin locus contraction needed for distal variable gene rearrangement. The mechanisms that control these crucial functions are unknown. We deleted the 25 amino-acid YY1 REPO domain necessary for YY1 PcG function, and used this mutant (YY1ΔREPO), to transduce bone marrow from YY1 conditional KO mice. While wild-type YY1 rescued B-cell development, YY1ΔREPO failed to rescue the B-cell lineage yielding reduced numbers of B lineage cells. Although the IgH rearrangement pattern was normal, there was a selective impact at the Igκ locus that showed a dramatic skewing of the expressed Igκ repertoire. We found that the REPO domain interacts with proteins from the condensin and cohesin complexes, and that YY1, EZH2 and condensin proteins co-localize at numerous sites across the Ig kappa locus. Knock-down of a condensin subunit protein or YY1 reduced rearrangement of Igκ Vκ genes suggesting a direct role for YY1-condensin complexes in Igκ locus structure and rearrangement.
| S-EPMC3630362 | biostudies-literature
Project description:Middle-down proteomics is an analytical approach whereby protein samples are digested with proteases such as Glu-C to generate large peptides (>3 kDa) that are then analyzed by mass spectrometry. This method is useful for characterizing high-molecular-weight proteins that are difficult to detect by top-down proteomics, in which intact proteins are analyzed by mass spectrometry. In this study, we applied GeLC-FAIMS-MS, a multidimensional separation workflow that combines gel-based prefractionation with LC-FAIMS Orbitrap mass spectrometry, for deep middle-down proteomics. Middle-down peptides obtained under the condition of optimized limited Glu-C digestion were first size-fractionated by polyacrylamide gel electrophoresis, followed by C4 reversed-phase liquid chromatography separation and additional ion mobility fractionation, resulting in a significant increase in peptide length detectable by mass spectrometry. In addition to global analysis, the GeLC-FAIMS concept can also be applied to targeted middle-down proteomics, where only proteins in the desired molecular weight range are gel-fractionated and their Glu-C digestion products are analyzed, as demonstrated by targeted analysis of integrins in exosomes. In-depth middle-down proteomics achieved by global and targeted GeLC-FAIMS-MS allows the exploration of proteoform information not covered by conventional top-down proteomics via increase in the number of detectable proteoforms and improvement in sequence coverage.
2024-11-20 | PXD041358 | Pride
Project description:Antigen receptor loci are organized into variable (V), diversity (D), and joining (J) elements that rearrange to generate diverse antigen receptor repertoires. Here, we identified an enhancer (E34) in the immunoglobulin kappa locus (Igκ) that instructed rearrangement of Vκ genes located in a sub-topologically associating domain (subTAD), including a Vκ gene encoding for antibodies targeting bacterial phosphorylcholine. E34 promoted the deposition of active histone marks across the E34 subTAD to instruct its nuclear repositioning from a V(D)J recombination-repressive compartment to a permissive one. E34-induced nuclear repositioning of the E34 subTAD promoted Vκ-Jκ interactions assisted by enhancer-associated epigenetic marks and de novo CTCF binding. Finally, we found that E34-instructed Vκ-Jκ rearrangement was essential to combat Streptococcus pneumoniae but not methicillin-resistant Staphylococcus aureus or influenza infections. These data show how enhancer-instructed chromatin topology mechanically pulls specific Vκ and Jκ genes into close physical proximity to generate distinct antibody repertoires to combat bacterial infection.
2022-12-05 | GSE193846 | GEO
Project description:Antigen receptor loci are organized into variable (V), diversity (D), and joining (J) elements that rearrange to generate diverse antigen receptor repertoires. Here, we identified an enhancer (E34) in the immunoglobulin kappa locus (Igκ) that instructed rearrangement of Vκ genes located in a sub-topologically associating domain (subTAD), including a Vκ gene encoding for antibodies targeting bacterial phosphorylcholine. E34 promoted the deposition of active histone marks across the E34 subTAD to instruct its nuclear repositioning from a V(D)J recombination-repressive compartment to a permissive one. E34-induced nuclear repositioning of the E34 subTAD promoted Vκ-Jκ interactions assisted by enhancer-associated epigenetic marks and de novo CTCF binding. Finally, we found that E34-instructed Vκ-Jκ rearrangement was essential to combat Streptococcus pneumoniae but not methicillin-resistant Staphylococcus aureus or influenza infections. These data show how enhancer-instructed chromatin topology mechanically pulls specific Vκ and Jκ genes into close physical proximity to generate distinct antibody repertoires to combat bacterial infection.
2022-12-05 | GSE193822 | GEO