The promoter regions of the T‐cell receptor V9 γ (TRGV9) and V2 δ (TRDV2) genes display short direct repeats but no TATA box

Dariavach, Piona; Lefranc, Marie‐Paule

doi:10.1016/0014-5793(89)81745-4

Cited by 14 publications

(3 citation statements)

References 49 publications

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“…A comparable preferential usage of the TRGJP (localized between TRGJP1 and TRGJ1 ) and the predominant expression of TRGV9-JP-C1 chain paired with a TRDV2-D-J-C in humans may be related to promoter characteristics [ 102 ]; thus, the same observation in both dolphins and humans supports an accurate determination of the TRGJ gene usage. As a consequence, the high frequency of TRGV1-J2/TRDV1-D1-J4 productive rearrangements in dolphins may represent a situation of oligoclonality comparable to that found in human TRGV9-JP/TRDV2-D-J T cells [ 103 ].…”

Section: The Trg Locus In Cetartiodactyla and Carnivora: The “Genementioning

confidence: 99%

Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals

Antonacci

Massari

Linguiti

et al. 2020

Genes

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T lymphocytes are the principal actors of vertebrates’ cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response.

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Section: The Trg Locus In Cetartiodactyla and Carnivora: The “Genementioning

confidence: 99%

Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals

Antonacci

Massari

Linguiti

et al. 2020

Genes

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“…However, we could not find any TATA-or CCAAT-like regulatory elements which are typical promotor motifs of many non-house-keeping genes. A number of other genes of the immune system also lack these elements, for instance Thy-1 (Giguere et al 1985), CD-2 (Diamond et al 1988), CD3 gamma (Dariavach and Lefranc 1989), CD3 delta (van den Elsen et al 1986), CD3 epsilon (Clevers et al 1988), and the pre-B-cell-specific genes V-pre B (Kudo and Melchers 1987) and lambda5 (Mfirtensson and Melchers 1994). Interestingly, there is another B1 repeat in the pTa upstream region stretching from position -463 to -332.…”

Section: Sequence and Genomic Organization Of The Pta Genementioning

confidence: 99%

Genomic structure and chromosomal location of the mouse pre-T-cell receptor alpha gene

Fehling¹,

Laplace²,

et al. 1995

Immunogenetics

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The mouse pre-T-cell receptor alpha (pT alpha) chain is a 33,000 M(r) glycoprotein expressed on the surface of immature thymocytes as a disulfide-linked heterodimer with the T-cell receptor beta (TCR beta) chain, and in association with proteins of the CD3 complex. The cDNA for pT alpha, isolated previously, encodes a type I transmembrane protein that is a member of the immunoglobulin (Ig) superfamily. Here we report the complete nucleotide sequence, the exon/intron structure, and the chromosomal location of the pTa gene. The gene spans about 8.4 kilobases (kb) and consists of four exons. Exon 1 encodes the 5' untranslated region, the leader peptide, and the first three amino acids of the mature protein. This exon is followed by a relatively long intron of 4.9 kb that contains many short interspersed repeats (SINEs) of the B1 and B2 family. The second exon encodes the extracellular Ig-like domain and exon 3 with just 45 base pairs the connecting peptide (CP), including the cysteine required for heterodimer formation. A similar exon/intron structure encoding corresponding parts of the mature polypeptide is found both in the Tcra and Tcrd constant region genes. The last exon encodes the transmembrane portion, the cytoplasmic tail, and about 540 nucleotides of 3' untranslated sequence, including a B2 repetitive element. In situ hybridization maps the pTa gene to the D/E1 region of mouse chromosome 17.

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“…The recombination of TRDV, or TRDD, with TRAJ genes does not violate the 12/23 rule (34) and has been proven experimentally to some extent (12,13). However, utilization of V genes in TRA recombination is thought to be governed at least in part by features of their promoters and chromatin accessibility (35)(36)(37)(38). While we found a tendency toward utilization of more downstream-located TRAJ genes, this was present in both TRAV-containing TRA chains and TRDV-TRA chains and we observed no apparent difference between the two types of alpha chains.…”

Section: Discussion and Outlookmentioning

confidence: 99%

Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires

Volkmar,

Fakhr,

Zens

et al. 2023

Front. Immunol.

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Here, we describe the identification of two T-cell receptors (TRs) containing TRDV genes in their TRA chains, the first one in human and the second one in mouse. First, using 5’RACE on a mixed lymphocyte-tumor cell culture (MLTC), we identified TRDV1 5’-untranslated region (UTR) and complete coding sequence rearranged productively to TRAJ24. Single-cell TR RNA sequencing (RNA-seq) of the MLTC, conducted to identify additional clonotypes, revealed that the analysis software detected the hybrid TRDV-TRAJ TRA (TRA) chain but excluded it from the final results. In a separate project, we performed TR sequencing of tumor-infiltrating lymphocytes (TILs) in a murine tumor model. Here, the predominant clonotype contained a TRA chain with a TRDV2-2-TRAJ49 rearrangement. Again, the hybrid TRA chain was not reported in the final results. Transfection of both TR cDNAs resulted in cell surface localization of TR together with CD3, suggesting a productive protein in both cases. Tumor recognition of the Homo sapiens (Homsap) TRDV1-containing TR could be demonstrated by IFN Gamma ELISA ELISpot kit, whereas the Mus musculus (Musmus) TR did not recognize a tumor-derived cell line. To determine whether the TRDV-containing TRA chains we detected were rare events or whether TRDV genes are commonly incorporated into TRA chains, we queried the NCBI Sequence Read Archive for TR single-cell RNA-seq data and analyzed 21 human and 23 murine datasets. We found that especially Homsap TRDV1, Musmus TRDV1, and to some extent Musmus TRDV2-2 are more commonly incorporated into TRA chains than several TRAV genes, making those TRDV genes a relevant contribution to TRA diversity. TRDV-containing TRA chains are currently excluded from the final results of V-(D)-J dataset analyses with the CellRanger software. We provide a work-around to avoid exclusion of those hybrid TRA chains from the final analysis results.

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The promoter regions of the T‐cell receptor V9 γ (TRGV9) and V2 δ (TRDV2) genes display short direct repeats but no TATA box

Cited by 14 publications

References 49 publications

Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals

Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals

Genomic structure and chromosomal location of the mouse pre-T-cell receptor alpha gene

Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires

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