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Three-way contact analysis characterizes the higher-order organization of the Tcra locus

ABSTRACT: Three-way contact analysis characterizes the higher-order organization of the Tcra locus

PROVIDER: PRJNA887738 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21824152_1.fastq.gz	Fastqsanger.gz
	SRR21824152_2.fastq.gz	Fastqsanger.gz
	SRR21824153_1.fastq.gz	Fastqsanger.gz
	SRR21824153_2.fastq.gz	Fastqsanger.gz
	SRR21824154_1.fastq.gz	Fastqsanger.gz

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Three-way contact analysis characterizes the higher-order organization of the Tcra locus

Project description:The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer Eα has been implicated in regulating the accessibility of Vα and Jα genes through long-range interactions during T cell antigen receptor gene Tcra rearrangements. However, direct evidence for Eα physically mediating the interaction of Vα and Jα genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher-order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multi-way contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal Jα genes, Vα genes, and Eα in CD4+CD8+ double-positive thymocytes. Notably, the INT2-TEAp loop emerged as a prominent structure likely responsible for bringing the proximal Jα genes and the Vα genes into proximity. Moreover, the enhancer Eα utilizes this loop to establish physical proximity with the proximal Vα gene region. This study provides insights into the higher-order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.

2022-11-28 | GSE214918 | GEO

Three-way contact analysis characterizes the higher order organization of the Tcra locus.

Project description:The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer Eα has been implicated in regulating the accessibility of Vα and Jα genes through long-range interactions during rearrangements of the T-cell antigen receptor gene Tcra. However, direct evidence for Eα physically mediating the interaction of Vα and Jα genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multiway contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal Jα genes, Vα genes and Eα in CD4+CD8+ double-positive thymocytes. Notably, the INT2-TEAp loop emerged as a prominent structure likely to be responsible for bringing the proximal Jα genes and the Vα genes into proximity. Moreover, the enhancer Eα utilizes this loop to establish physical proximity with the proximal Vα gene region. This study provides insights into the higher order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.

| S-EPMC10516640 | biostudies-literature

E protein binding at the Tcra enhancer promotes Tcra repertoire diversity

Project description:The Tcra gene enhancer (Eα) is required for Tcra rearrangment. Our study assesses the role of E protein binding at Eα. Tcra repertoire sequencing was used to determine whether loss of Eα E protein binding sites alters recombination at Tcra.

2023-03-16 | GSE227164 | GEO

Tcrd rearrangement redirects a processive Tcra recombination program to expand the Tcra repertoire

Project description:The Tcra-Tcrd locus undergoes Tcrd rearrangement in DN thymocytes followed by primary and secondary Tcra rearrangements in DP thymocytes. Here we reveal the mechanisms underpinning combinatorial diversity in the Tcra repertoire. We show that V-alpha and J-alpha segments on individual Tcra alleles are used in stepwise and coordinated proximal-to-distal progressions during primary and secondary rearrangements, substantially constraining combinatorial diversity. Notably, Tcrd recombination in DN thymocytes diversifies the Tcra repertoire by truncating the V-alpha array to permit otherwise disfavored V-J combinations. Such diversification is important, because Trav1-Traj33+ mucosa-associated invariant T cells are depleted when Tcrd rearrangement is impaired. Our results reveal an important biological advantage conferred by the nested organization of Tcrd and Tcra gene segments.

2017-06-06 | GSE95826 | GEO

in situ HiPore-C reveals higher-order 3D genome folding principles

Project description:Eukaryotic genomes are folded into three-dimensional (3D) hierarchical architectures consisting of multi-way chromatin contacts that are involved in complex gene regulation. High-throughput chromosome conformation capture (Hi-C), chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) , and methods similar to these two rely on pairwise ligation of fragments in proximity in a population of cells, thus fail to reveal multi-way chromatin interactions in single allele at single fragment resolution. To explore higher-order chromatin interaction genome-widely, a straightforward strategy is integrating multi-fragment ligates preparation with third-generation sequencing technology. To achieve this purpose, we developed a protocol of in situ high throughput multi-way contact long read Pore-C sequencing (in situ HiPore-C) We performed genome-wide multi-way contact profiling analysis using data obtained from in situ HiPore-C sequencing of GM12878 and K562 cell lines.

2023-01-20 | GSE202539 | GEO

E protein binding at the Tcra enhancer promotes Tcra repertoire diversity

Project description:E protein binding at the Tcra enhancer promotes Tcra repertoire diversity

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Trav15-dv6 family Tcrd rearrangements diversify the Tcra repertoire

Project description:Dauphars et al. show that prior Tcrd rearrangement is essential for a combinatorially diverse Tcra repertoire in mouse thymocytes. Trav15-dv6 family Tcrd rearrangements are critical for Tcra repertoire formation because of their central and distal locations in the Va-Vd array.

2021-10-21 | GSE186044 | GEO

A role of the CTCF binding site at enhancer Ea in Tcra rearrangement

Project description:We found that the CTCF binding site (named as EACBE) at the enhancer Eα of Tcra is essential for normal Tcra rearrangement.The EACBE deletion impaired the TAD structure of the 3’ region of the Tcra/d locus and the interactions between the proximal Vα genes and the Jα genes without changing the accessibility of the Jα array.

2020-02-13 | GSE145147 | GEO

Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers.

Project description:V(D)J recombination is essential for generating a diverse array of B and T cell receptors that can recognize and combat foreign antigens. As with any recombination event, tight control is essential to prevent the occurrence of genetic anomalies that drive cellular transformation. One important aspect of regulation is directed targeting of the RAG recombinase. Indeed, RAG accumulates at the 3' end of individual antigen receptor loci poised for rearrangement; however, it is not known whether focal binding is involved in regulating cleavage, and what mechanisms lead to enrichment of RAG in this region. Here, we show that monoallelic looping out of the 3' end of the T cell receptor ? (Tcra) locus, coupled with transcription and increased chromatin/nuclear accessibility, is linked to focal RAG binding and ATM-mediated regulation of monoallelic cleavage on looped-out 3' regions. Our data identify higher-order loop formation as a key determinant of directed RAG targeting and the maintenance of genome stability.

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ROR t directs upregulation of RAG gene expression in DP thymocytes and serves as a multi-faceted regulator of the Tcra repertoire.

Project description:Naik et al. show that RAG gene upregulation in DP Thymocytes is controlled by DPASE, a DP-specific open chromatin region in RAG locus. Reduced RAG expression in DPASE KO mice result delayed and incomplete Tcra recombination. Transcription factor RORyt binds to DPASE and Tcra enhancer to regulate Tcra recombination in DP thymocytes.

2023-02-20 | GSE225627 | GEO

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