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Trav15-dv6 family Tcrd rearrangements diversify the Tcra repertoire

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE186044 | GEO | 2021/10/21

REPOSITORIES: GEO

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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

Trav15-dv6 family Tcrd rearrangements diversify the Tcra repertoire

Project description:Trav15-dv6 family Tcrd rearrangements diversify the Tcra repertoire

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A discrete chromatin loop in the murine Tcra/Tcrd locus shapes the TCRδ and TCRα repertoires

Project description:The Tcra/Tcrd locus undergoes V(D)J recombination in CD4−CD8− double-negative (DN) thymocytes and CD4+CD8+ double-positive (DP) thymocytes to generate diverse TCRδ and TCRα repertoires, respectively. Here we reveal a Tcra/Tcrd locus chromatin interaction network in DN thymocytes that is formed by interactions between CTCF-binding elements (CBEs). Disruption of a discrete chromatin loop encompassing the Dδ, Jδ and Cδ gene segments allows a single Vδ segment to frequently contact and rearrange to Dδ and Jδ segments and dominate the adult TCRδ repertoire. Disruption of this loop also narrows the TCRα repertoire, which, we believe, follows as a consequence of the restricted TCRδ repertoire. Hence, a single CTCF-mediated chromatin loop directly regulates TCRδ diversity and indirectly regulates TCRα diversity. Examination of chromatin loops by 4C-seq from 4 viewpoints in two lymphoid cell compartments: CD4-CD8- thymocytes and naïve B splenocytes.

2015-08-10 | E-GEOD-67442 | biostudies-arrayexpress

A discrete chromatin loop in the murine Tcra/Tcrd locus shapes the TCRδ and TCRα repertoires

2015-08-10 | GSE67442 | GEO

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: Not available

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An ectopic CTCF binding element disturbs VÎ´ usage at the mouse Tcra-Tcrd locus by regulating contact between VÎ´ and DÎ´ gene segments

Project description:Chromatin looping mediated by the CCCTC binding factor CTCF regulates V(D)J recombination at antigen receptor loci. CTCF-mediated looping can influence recombination signal sequence accessibility by regulating enhancer activation of germline promoters. CTCF-mediated looping has also been shown to limit directional tracking of the RAG recombinase along chromatin, and to regulate through-space interactions between recombination signal sequences, independent of the RAG recombinase. However, in all prior instances in which CTCF-mediated looping was shown to influence V(D)J recombination, it was not possible to fully resolve the relative contributions to the V(D)J recombination phenotype of changes in accessibility, RAG-tracking, and RAG-independent long-distance interactions. Here, to assess mechanisms by which CTCF-mediated looping can impact V(D)J recombination, we introduced an ectopic CTCF binding element (CBE) immediately downstream of EÎ´ in the murine Tcra-Tcrd locus. The ectopic CBE impaired inversional rearrangement of Trdv5 in the absence of measurable effects on Trdv5 transcription and chromatin accessibility. Moreover, although the ectopic CBE limited directional RAG tracking from the Tcrd recombination center, such tracking cannot account for Trdv5-to-Trdd2 inversional rearrangement. Rather, the defect in Trdv5 rearrangement could only be attributed to a reconfigured chromatin loop organization that limited RAG-independent through-space interactions between the Trdv5 and Trdd2 RSSs. We conclude that CTCF can regulate V(D)J recombination by segregating RSSs into distinct loop domains and inhibiting RSS synapsis, independent of any effects on transcription, RSS accessibility and RAG tracking. RAG-initiatd Tcrd D segment rearrangements in developing thymocytes were generated by deep sequencing using illumine Miseq

2016-09-02 | E-GEOD-81351 | biostudies-arrayexpress

The Role of Satb1 in Shaping the Repertoire of T Cell Receptor Genes

Project description:To explore the role of Satb1 in rearrangement and repertoire of TCR genes, we used Satb1contional knockout micwhich the Satb1 gene was deleted in long term hematopoietic stem cells. We applied 5ʹRACE (rapid amplification of cDNA ends) PCR technique to generate deep sequencing libraries of Tcrd, Tcrg, Tcrb, and Tcra cDNA by using a single set of primers for each TCR gene. We obtained millions of TCR sequences and unraveled the complexity of T-cell diversity. Our experimental evidence demonstrates that Satb1 has substantial influences on the TCR repertoire.

2020-07-10 | GSE154069 | GEO

MHC-independent αβ T cells replace epidermal and dermal γδ T cells in Tcrd-/- mice

Project description:In Tcrd-/- mice, dendritic epidermal T cells (DETC) are known to be replaced by a DETC-population expressing αβ TCR. Here, the TCR-repertoire from Tcrd-/- mouse skin T cells was compared to the one from WT mice. The analysis revealed the existence of T cells expressing MHC-independent αβ TCR and replacing the missing γδ T cells in Tcrd-/- mouse epidermis and dermis.

2021-12-21 | GSE168123 | GEO

An ectopic CTCF binding element disturbs Vδ usage at the mouse Tcra-Tcrd locus by regulating contact between Vδ and Dδ gene segments

Project description:Chromatin looping mediated by the CCCTC binding factor CTCF regulates V(D)J recombination at antigen receptor loci. CTCF-mediated looping can influence recombination signal sequence accessibility by regulating enhancer activation of germline promoters. CTCF-mediated looping has also been shown to limit directional tracking of the RAG recombinase along chromatin, and to regulate through-space interactions between recombination signal sequences, independent of the RAG recombinase. However, in all prior instances in which CTCF-mediated looping was shown to influence V(D)J recombination, it was not possible to fully resolve the relative contributions to the V(D)J recombination phenotype of changes in accessibility, RAG-tracking, and RAG-independent long-distance interactions. Here, to assess mechanisms by which CTCF-mediated looping can impact V(D)J recombination, we introduced an ectopic CTCF binding element (CBE) immediately downstream of Eδ in the murine Tcra-Tcrd locus. The ectopic CBE impaired inversional rearrangement of Trdv5 in the absence of measurable effects on Trdv5 transcription and chromatin accessibility. Moreover, although the ectopic CBE limited directional RAG tracking from the Tcrd recombination center, such tracking cannot account for Trdv5-to-Trdd2 inversional rearrangement. Rather, the defect in Trdv5 rearrangement could only be attributed to a reconfigured chromatin loop organization that limited RAG-independent through-space interactions between the Trdv5 and Trdd2 RSSs. We conclude that CTCF can regulate V(D)J recombination by segregating RSSs into distinct loop domains and inhibiting RSS synapsis, independent of any effects on transcription, RSS accessibility and RAG tracking.

2016-09-02 | GSE81351 | GEO

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