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Transcription 2015Tcra/Tcrd includes 2 genes with distinct developmental programs controlled by 2 distant enhancers, Eα and Eδ. These enhancers work as a developmental switch during... (Review)
Review
Tcra/Tcrd includes 2 genes with distinct developmental programs controlled by 2 distant enhancers, Eα and Eδ. These enhancers work as a developmental switch during thymocyte development and they are essential for generation of αβ and γδ T-lymphocytes. Tcra and Tcrd transit from an unrearranged configuration to a rearranged configuration during T-cell development. Eα and Eδ are responsible for transcription of their respective unrearranged genes in thymocytes but are dispensable for such functions in the context of the rearranged genes in mature T-cells. Interestingly, Eα activates transcription of the rearranged Tcrd in γδ T-lymphocytes but it is inactive in αβ T-lymphocytes.
Topics: Animals; Enhancer Elements, Genetic; Humans; Models, Genetic; Receptors, Antigen, T-Cell, alpha-beta; Receptors, Antigen, T-Cell, gamma-delta; T-Lymphocytes; Thymocytes; Transcription, Genetic; V(D)J Recombination
PubMed: 26230488
DOI: 10.1080/21541264.2015.1078429 -
Blood Aug 1986In this review the genomic structure and the RNA transcripts of the alpha and beta chain of the T cell antigen receptor have been discussed. Studies of the structure of... (Review)
Review
In this review the genomic structure and the RNA transcripts of the alpha and beta chain of the T cell antigen receptor have been discussed. Studies of the structure of TcR beta in hematologic malignancies have revealed rearrangement in almost all of the T cell malignancies and a small proportion of non-T cell malignancies. In addition, clonal involvement of T cells in diseases such as Hodgkin's disease, angioimmunoblastic lymphadenopathy, and chronic T cell lymphocytosis have been observed. The study of the structure of the TcR beta gene is thus a useful tool for identifying clonal expansions of cells and in conjunction with studies of the immunoglobulin gene structure, and cell surface markers a useful tool for identifying cell lineage. At the present time the evaluation of the structure of the alpha chain genes has not been as fruitful. However, chromosome translocations involving the TcR alpha chain genes have been recognized and, in one case, this rearrangement has been in association with a known oncogene. With the isolation of more probes to the alpha chain region it should be possible to test its utility in identifying clonal populations and cell lineage. The recent isolation of the gamma gene of the T cell will also permit such studies. Preliminary results of studies carried out with a probe to the gamma chain gene of the T cell have paralleled results obtained with the TcR beta probe (unpublished observation).
Topics: Chromosomes, Human, 6-12 and X; Cloning, Molecular; Genotype; Hodgkin Disease; Humans; Immunoblastic Lymphadenopathy; Immunoglobulin J-Chains; Immunoglobulin Light Chains; Immunoglobulin alpha-Chains; Leukemia, Lymphoid; Leukemia, Myeloid, Acute; Lymphatic Diseases; Lymphocytosis; Lymphoma; Oncogenes; Receptors, Antigen, T-Cell; Recombination, Genetic; Sezary Syndrome; T-Lymphocytes; Translocation, Genetic
PubMed: 3089348
DOI: No ID Found -
The EMBO Journal Apr 2012EMBO J 31 7, 1666–1678 (2012); February 28 2012 By sequencing tens of millions of TCRα transcripts from naive mouse CD8 T cells, Genolet et al (2012) show that the...
EMBO J 31 7, 1666–1678 (2012); February 28 2012 By sequencing tens of millions of TCRα transcripts from naive mouse CD8 T cells, Genolet et al (2012) show that the TCRα repertoire is at least as diverse as the TCRβ repertoire. This overturns a long held view in the field that recombination of the locus occurs in a co-ordinate sequential bidirectional manner that relies on proximity of Vα and Jα gene segments. The observation that rearrangement of all possible Vα-Jα combinations can occur is consistent with an alternative model in which intralocus loop formation/locus contraction enables an opportunity for all Vα gene segments to recombine with Jα gene segments.
Topics: Animals; CD8-Positive T-Lymphocytes; Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor; Genes, T-Cell Receptor alpha; Recombination, Genetic
PubMed: 22415367
DOI: 10.1038/emboj.2012.64 -
Proceedings of the National Academy of... Dec 2012Antigen receptor locus V(D)J recombination requires interactions between widely separated variable (V), diversity (D), and joining (J) gene segments, but the mechanisms...
Antigen receptor locus V(D)J recombination requires interactions between widely separated variable (V), diversity (D), and joining (J) gene segments, but the mechanisms that generate these interactions are not well understood. Here we assessed mechanisms that direct developmental stage-specific long-distance interactions at the Tcra/Tcrd locus. The Tcra/Tcrd locus recombines Tcrd gene segments in CD4(-)CD8(-) double-negative thymocytes and Tcra gene segments in CD4(+)CD8(+) double-positive thymocytes. Initial V(α)-to-J(α) recombination occurs within a chromosomal domain that displays a contracted conformation in both thymocyte subsets. We used chromosome conformation capture to demonstrate that the Tcra enhancer (E(α)) interacts directly with V(α) and J(α) gene segments distributed across this domain, specifically in double-positive thymocytes. Moreover, E(α) promotes interactions between these V(α) and J(α) segments that should facilitate their synapsis. We found that the CCCTC-binding factor (CTCF) binds to E(α) and to many locus promoters, biases E(α) to interact with these promoters, and is required for efficient V(α)-J(α) recombination. Our data indicate that E(α) and CTCF cooperate to create a developmentally regulated chromatin hub that supports V(α)-J(α) synapsis and recombination.
Topics: Animals; Base Sequence; CCCTC-Binding Factor; Chromatin; DNA Primers; Enhancer Elements, Genetic; Genes, T-Cell Receptor alpha; Genes, T-Cell Receptor delta; Mice; Mice, 129 Strain; Mice, Inbred C57BL; Mice, Knockout; Mice, Transgenic; Models, Genetic; Models, Immunological; Repressor Proteins; T-Lymphocytes; V(D)J Recombination
PubMed: 23169622
DOI: 10.1073/pnas.1214131109 -
Expression of unique gene signature distinguishes TCRαβ /BCR dual expressers from CD3 CD14 doublets.Cytometry. Part a : the Journal of the... Apr 2022Increasing evidence shows pathophysiological significance of rare immune cells, necessitating the need for reliable and proper methods for their detection and analysis....
Increasing evidence shows pathophysiological significance of rare immune cells, necessitating the need for reliable and proper methods for their detection and analysis. We have recently identified a new lymphocyte that coexpresses lineage markers of T- and B-cells including T cell receptor and B cell receptor (called dual expressers, DEs). Because of the peculiar phenotype of DEs, we used multiple techniques to authenticate their identity (fluorescence-activated cell sorting [FACS], scRNAseq, EBV cell lines, and imaging flow cytometry). In an recent article published in this journal, Burel and colleagues successfully detected DEs using FACS and imaging microscopy. Yet they claimed, based on the profile of what they called naturally occurring CD3 CD14 T cell/monocyte complexes that the scRNAseq signature of DEs resembles that of cell-cell complexes. Serious flaws in their analysis, however, invalidate their conclusions. Unlike the CD3 CD14 complexes, DEs have a distinct identity due to expression of a unique set of signature genes. Without a clear explanation, Burel and colleagues excluded these genes from their analysis, thereby effectively stripped DEs from their identity. Inclusion of these genes as described in this communication restores the identity of DEs. Moreover, contrary to the claim of Burel and colleagues, B- and T-cell specific genes are similarly expressed in DE cells.
Topics: B-Lymphocytes; CD3 Complex; Flow Cytometry; Lymphocytes; Receptors, Antigen, T-Cell, alpha-beta; T-Lymphocytes
PubMed: 35092640
DOI: 10.1002/cyto.a.24542 -
The Journal of Experimental Medicine Aug 2005Murine Tcrd and Tcra gene segments reside in a single genetic locus and undergo recombination in CD4- CD8- (double negative [DN]) and CD4+ CD8+ (double positive [DP])...
Murine Tcrd and Tcra gene segments reside in a single genetic locus and undergo recombination in CD4- CD8- (double negative [DN]) and CD4+ CD8+ (double positive [DP]) thymocytes, respectively. TcraTcrd locus variable gene segments are subject to complex regulation. Only a small subset of approximately 100 variable gene segments contributes substantially to the adult TCRdelta repertoire. Moreover, although most contribute to the TCRalpha repertoire, variable gene segments that are Jalpha proximal are preferentially used during primary Tcra recombination. We investigate the role of local chromatin accessibility in determining the developmental pattern of TcraTcrd locus variable gene segment recombination. We find variable gene segments to be heterogeneous with respect to acetylation of histones H3 and H4. Those that dominate the adult TCRdelta repertoire are hyperacetylated in DN thymocytes, independent of their position in the locus. Moreover, proximal variable gene segments show dramatic increases in histone acetylation and germline transcription in DP thymocytes, a result of super long-distance regulation by the Tcra enhancer. Our results imply that differences in chromatin accessibility contribute to biases in TcraTcrd locus variable gene segment recombination in DN and DP thymocytes and extend the distance over which the Tcra enhancer can regulate chromatin structure to a remarkable 525 kb.
Topics: Acetylation; Animals; CD4-Positive T-Lymphocytes; CD8-Positive T-Lymphocytes; Chromatin; Chromatin Assembly and Disassembly; Enhancer Elements, Genetic; Gene Expression Regulation; Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor; Gene Rearrangement, delta-Chain T-Cell Antigen Receptor; Genes, T-Cell Receptor alpha; Genes, T-Cell Receptor delta; Histones; Mice; Mice, Knockout; Quantitative Trait Loci; Recombination, Genetic; Thymus Gland; Transcription, Genetic
PubMed: 16087716
DOI: 10.1084/jem.20050680 -
The Journal of Clinical Investigation Apr 1988We have analyzed the configuration of the T cell receptor (TCR) alpha gene using newly developed genomic joining region (J alpha) probes, which cover approximately 80 kb...
We have analyzed the configuration of the T cell receptor (TCR) alpha gene using newly developed genomic joining region (J alpha) probes, which cover approximately 80 kb of the J alpha region upstream from the constant region in 19 patients with T cell acute lymphoblastic leukemia (T-ALL) and in three CD3- leukemic T cell lines (HSB2, CEM, and MOLT4). In parallel, transcription of the TCR-alpha, beta, and gamma genes was examined in 11 of these patients and in the T cell lines. All T-ALL and the three T cell lines exhibited both TCR-gamma and beta gene rearrangements. 8 of 10 T-ALL and all T cell lines expressed TCR-gamma transcripts. All samples tested expressed both TCR-beta and CD3-gamma transcripts. TCR alpha transcripts were only observed in CD3+ T-ALL but not in CD3- T-ALL or the CD3- cell lines. Among the CD3+ T-ALL, eight had TCR-alpha gene rearrangements. In addition, TCR-alpha gene rearrangements were detected in one CD3- T-ALL and all three T cell lines. These leukemic cells may represent a transient stage between rearrangement and expression and provide an opportunity for analyzing the mechanism regulating the expression of the TCR-alpha gene.
Topics: DNA, Neoplasm; Gene Expression Regulation; Genes; Humans; Leukemia, Lymphoid; Receptors, Antigen, T-Cell; Tumor Cells, Cultured
PubMed: 3162460
DOI: 10.1172/JCI113453 -
PloS One 2015The transformer (tra) gene appears to act as the genetic switch that promotes female development by interaction with the transformer2 (tra-2) gene in several dipteran...
The transformer (tra) gene appears to act as the genetic switch that promotes female development by interaction with the transformer2 (tra-2) gene in several dipteran species including the Medfly, housefly and Drosophila melanogaster. In this study, we describe the isolation, expression and function of tra and tra-2 in the economically important agricultural pest, the oriental fruit fly, Bactrocera dorsalis (Hendel). Bdtra and Bdtra-2 are similar to their homologs from other tephritid species. Bdtra demonstrated sex-specific transcripts: one transcript in females and two transcripts in males. In contrast, Bdtra-2 only had one transcript that was common to males and females, which was transcribed continuously in different adult tissues and developmental stages. Bdtra-2 and the female form of Bdtra were maternally inherited in eggs, whereas the male form of Bdtra was not detectable until embryos of 1 and 2 h after egg laying. Function analyses of Bdtra and Bdtra-2 indicated that both were indispensable for female development, as nearly 100% males were obtained with embryonic RNAi against either Bdtra or Bdtra-2. The fertility of these RNAi-generated males was subsequently tested. More than 80% of RNAi-generated males could mate and the mated females could lay eggs, but only 40-48.6% males gave rise to progeny. In XX-reversed males and intersex individuals, no clear female gonadal morphology was observed after dissection. These results shed light on the development of a genetic sexing system with male-only release for this agricultural pest.
Topics: Animals; Diptera; Female; Gene Silencing; Insect Proteins; Male; RNA-Binding Proteins; Sex Determination Processes; Sex Differentiation
PubMed: 26057559
DOI: 10.1371/journal.pone.0128892 -
PloS One 2015Every person carries a vast repertoire of CD4+ T-helper cells and CD8+ cytotoxic T cells for a healthy immune system. Somatic VDJ recombination at genomic loci that...
Every person carries a vast repertoire of CD4+ T-helper cells and CD8+ cytotoxic T cells for a healthy immune system. Somatic VDJ recombination at genomic loci that encode the T-cell receptor (TCR) is a key step during T-cell development, but how a single T cell commits to become either CD4+ or CD8+ is poorly understood. To evaluate the influence of TCR sequence variation on CD4+/CD8+ lineage commitment, we sequenced rearranged TCRs for both α and β chains in naïve T cells isolated from healthy donors and investigated gene segment usage and recombination patterns in CD4+ and CD8+ T-cell subsets. Our data demonstrate that most V and J gene segments are strongly biased in the naïve CD4+ and CD8+ subsets with some segments increasing the odds of being CD4+ (or CD8+) up to five-fold. These V and J gene associations are highly reproducible across individuals and independent of classical HLA genotype, explaining ~11% of the observed variance in the CD4+ vs. CD8+ propensity. In addition, we identified a strong independent association of the electrostatic charge of the complementarity determining region 3 (CDR3) in both α and β chains, where a positively charged CDR3 is associated with CD4+ lineage and a negatively charged CDR3 with CD8+ lineage. Our findings suggest that somatic variation in different parts of the TCR influences T-cell lineage commitment in a predominantly additive fashion. This notion can help delineate how certain structural features of the TCR-peptide-HLA complex influence thymic selection.
Topics: CD4-Positive T-Lymphocytes; CD8-Positive T-Lymphocytes; Cell Differentiation; Cell Lineage; Genes, T-Cell Receptor; Genes, T-Cell Receptor alpha; Genes, T-Cell Receptor beta; Genetic Variation; HLA Antigens; Humans; Receptors, Antigen, T-Cell
PubMed: 26517366
DOI: 10.1371/journal.pone.0140815 -
BMC Immunology Oct 2016High-throughput sequencing of T cell receptor (TCR) genes is a powerful tool for analyses of antigen specificity, clonality and diversity of T lymphocytes. Here, we...
A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains.
BACKGROUND
High-throughput sequencing of T cell receptor (TCR) genes is a powerful tool for analyses of antigen specificity, clonality and diversity of T lymphocytes. Here, we developed a new TCR repertoire analysis method using 454 DNA sequencing technology in combination with an adaptor-ligation mediated polymerase chain reaction (PCR). This method allows the amplification of all TCR genes without PCR bias. To compare gene usage, diversity and similarity of expressed TCR repertoires among individuals, we conducted next-generation sequencing (NGS) of TRA and TRB genes in peripheral blood mononuclear cells from 20 healthy human individuals.
RESULTS
From a total of 267,037 sequence reads from 20 individuals, 149,216 unique sequence reads were identified. Preferential usage of several V and J genes were observed while some recombinations of TRAV with TRAJ appeared to be restricted. The extent of TCR diversity was not significantly different between TRA and TRB, while TRA repertoires were more similar between individuals than TRB repertoires were. The interindividual similarity of TRA depended largely on the frequent presence of shared TCRs among two or more individuals. A publicly available TRA had a near-germline TCR with a shorter CDR3. Notably, shared TRA sequences, especially those shared among a large number of individuals', often contained TCRα related with invariant TCRα derived from invariant natural killer T cells and mucosal-associated invariant T cells.
CONCLUSION
These results suggest that retrieval of shared TCRs by NGS would be useful for the identification of potential new invariant TCRα chains. This NGS method will enable the comprehensive quantitative analysis of TCR repertoires at a clonal level.
Topics: Adult; Aged; Clone Cells; Computational Biology; Female; Genetic Variation; Healthy Volunteers; High-Throughput Nucleotide Sequencing; Humans; Japan; Leukocytes, Mononuclear; Male; Middle Aged; Polymerase Chain Reaction; Receptors, Antigen, T-Cell, alpha-beta
PubMed: 27729009
DOI: 10.1186/s12865-016-0177-5