Human T-cell receptor variable gene segment families

Multiple DNA and protein sequence alignments have been constructed for the human T-cell receptor /, , and (TCRA/D, B, and G) variable (V) gene segments. The traditional classification into subfamilies was confirmed using a much larger pool of sequences. For each sequence, a name was derived which complies with the standard nomenclature. The traditional numbering of V gene segments in the order of their discovery was continued and changed when in conflict with names of other segments. By discriminating between alleles at the same locus versus genes from different loci, we were able to reduce the number of more than 150 different TCRBV sequences in the database to a repertoire of only 47 functional TCRBV gene segments. An extension of this analysis to the over 100 TCRAV sequences results in a predicted repertoire of 42 functional TCRAV gene segments. Our alignment revealed two residues that distinguish between the highly homologous V and V, one at a site that in V_H contacts the constant region, the other at the interface between immunoglobulin V_H and V_L. This site may be responsible for restricted pairing between certain V and V chains. On the other hand, V and V appear to be related by the fact that their CDR2 legnth is increased by four residues as compared with that of V/ peptides.The alignment data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the aligmment number DS23485. The data are available by the EBI FTP server and file serverCorrespondence with corrections or new information concerning the TCRV sequences is strongly encouraged.     

Mouse T-cell receptor variable gene segment families

All mouse T-cell receptor /, , and variable (Tcra/d, b-, and g-V) gene segments were aligned to compare the sequences with one another, to group them into subfamilies, and to derive a name which complies with the standard nomenclature. It was necessary to change the names of some V gene segments because they conflicted with those of other segments. The traditional classification into subfamilies was re-evaluated using a much larger pool of sequences. In the mouse, most V gene segments can be grouped into subfamilies of closely related genes with significantly less similarity between different subfamilies.The alignment data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the alignment number DS23485. The data are available by the EBI FTP server and file serverCorrespondence with corrections or new information concerning the TCRV sequences is strongly encouraged.     

Molecular genotyping of human T-cell antigen receptor variable gene segments

The gene complex encoding the chain of the T-cell antigen receptor (Tcr) in man was previously reported to contain a restriction fragment length polymorphism (RFLP) involving a single Bgl II site adjacent to the second constant region gene. This RFLP allowed assignment of Tcr genotypes in certain human families. In the present study, two different RFLP in a V gene family were detected using the murine probe V8.1 in genomic DNA samples digested with the restriction endonucleases Hind III and Bam HI. Use of these RFLP to mark the V gene complex allowed complete haplotype assignment in four of seven families studied and provided support for linkage of the V gene complex to the constant region genes. Different combinations of the C and two V region markers can result in eight possible distinct haplotypes. The observation of all but one of the eight possible haplotypes in parents of the families studied suggests that recombination events occur between the C and V region and among members of the V region subfamily marked by the V8.1 probe. These markers can be used for mapping studies of the V gene complex in man and will allow an appraisal of possible associations between Tcr genes and disease susceptibility.Abbreviations used in this paper: Tcr T-cell antigen receptor - RFLP restriction fragment length polymorphism - C2 second Tcr constant region gene - V Variable - C constant - J joining - D diversity     

Location of mouse and human genes corresponding to conserved canine olfactory receptor gene subfamilies

Olfactory receptors are G protein-coupled, seven-transmembrane-domain proteins that are responsible for binding odorants in the nasal epithelium. They are encoded by a large gene family, members of which are organized in several clusters scattered throughout the genomes of mammalian species. Here we describe the mapping of mouse sequences corresponding to four conserved olfactory receptor genes, each representing separate, recently identified canine gene subfamilies. Three of the four canine genes detected related gene clusters in regions of mouse Chromosomes (Chrs) 2, 9, and 10, near previously mapped mouse olfactory genes, while one detected a formerly unidentified gene cluster located on mouse Chr 6. In addition, we have localized two human gene clusters with homology to the canine gene, CfOLF4, within the established physical map of Chr 19p. Combined with recently published studies, these data link the four conserved olfactory gene subfamilies to homologous regions of the human, dog, and mouse genomes. Received: 10 September 1997 / Accepted: 29 December 1997     

Characterization of the T-cell receptor gamma locus and analysis of the variable gene segment expression in rabbit

The genomic organization and expression of genes of the T-cell receptor gamma (TRG) locus are described for mice and humans, but not for species such as rabbits (Oryctolagus cuniculus), in which T cells compose a sizeable proportion of T cells in the periphery. We cloned 200 kb of the rabbit TRG locus and determined the TRGV gene usage in adult and newborn rabbits by RT-PCR. We identified two TRGJ genes, one TRGC gene, and 22 TRGV genes, all of which encoded functional variable regions. One TRGV gene is the unique member of the TRGV2 subgroup, whereas the other genes belong to the TRGV1 subgroup. Evolutionary analyses of TRGV1 genes identified three distinct groups that can be explained by separate duplication events in the rabbit genome. Evidence of gene conversion between TRGV1.1 and TRGV1.6 was observed. Both TRGV1 and TRGV2 subgroup genes were expressed in the spleen, intestine, and appendix of adult rabbits, and the repertoire of TRGV genes expressed in these tissues was similar. In these tissues from newborns, and in skin from adults, only the genes from the TRGV1 subgroup were expressed. Greater TRGV-J junctional diversity was found in tissues from adult compared to newborn rabbits. Our analyses indicate rabbits have a larger germ line encoded TRG repertoire compared with that of mice and humans. In addition, we found TRGV gene usage is alike in most tissues of rabbits similar to that found in humans but in contrast to that found in mice.Electronic SupplementaryMaterial Supplementary material is available for this article at The nucleotide sequence data reported in this article have been submitted to GenBank and are assigned the accession numbers AY748325–AY748348     

The extent of the human germline T-cell receptor V beta gene segment repertoire

An assessment of the size of the human TCRBV gene segment repertoire based on the identification of TCRBV gene segments in genomic DNA was undertaken. PCR amplification from cloned and uncloned genomic DNA sources, nucleotide sequencing, Southern blot hybridization, and cosmid cloning were used to identify TCRBV gene segments in multiple unrelated individuals. The key advantages to this approach were: (1) TCRBV gene segments which are expressed only at very low levels in cDNA libraries were still detectable, and (2) it was possible to discriminate between alleles at the same locus vs products of different loci. A total of 63 unique TCRBV gene segments were identified and sequenced. Six of these TCRBV gene segments had not been previously described. Thirty-four cosmid clones containing 51 of the 63 identified TCRBV gene segments were isolated and screened for the presence of additional novel TCRBV subfamily members. These results, obtained by a variety of complementary approaches, indicate that the human TCRBV gene segments of which 52 are functional. The availability of the majority of these TCRBV gene segments on cosmid clones should facilitate further investigation of germline TCRBV gene segment polymorphism and putative disease associations.     

Designing exons for human olfactory receptor gene subfamilies using a mathematical paradigm

Ligands for only two human olfactory receptors are known. One of them, OR1D2, binds to Bourgeonal, a volatile chemical constituent of the fragrance of the mythical flower, Lily of the valley or Our Lady’s tears, Convallaria majalis (also the national flower of Finland). OR1D2, OR1D4 and OR1D5 are three full-length olfactory receptors present in an olfactory locus in the human genome. These receptors are more than 80% identical in DNA sequences and have 108 base pair mismatches among them. Apparently, these mismatch positions show no striking pattern using computer pattern recognition tools. In an attempt to find a mathematical rule in those mismatches, we find that an L-system generated sequence can be inserted into the OR1D2 subfamily-specific star model and novel full-length olfactory receptors can be generated. This remarkable mathematical principle could be utilized for making new subfamily olfactory receptor members from any olfactory receptor subfamily. The aroma and electronic nose industry might utilize this rule in future.     

Sequence and diversity of variable gene segments coding for rabbit T-cell receptor beta chains

The nucleotide sequences of 11 variable gene segments coding for rabbit T-cell receptor beta (Tcrb-V) chains were determined by directly sequencing fragments amplified by the cassette-ligation mediated polymerase chain reaction (CLM-PCR) and by modified anchor PCR without the cloning procedure. The nucleotide sequences in two of these 11 rabbit Tcrb-V gene segments coincided with those in two of the four rabbit Tcrb-V gene segments previously reported; the others have not been described. The percentage similarity of each nucleotide sequence of the 11 rabbit Tcrb-V gene segments was analyzed and the segments were divided into nine families, which were homologous to nine human families (Vb 2, 3, 4, 5, 7, 8, 10, 18, and 22), respectively.The nucleotide sequence data reported in this paper have been submitted to the DDBJ, EMBL, and GenBank nucleotide sequence databases and have been assigned the accession numbers D17416-D17426.     

Restriction fragment length polymorphisms of the mouse T-cell receptor gene families

We have studied the restriction fragment length polymorphisms (RFLPs) found in the germline T-cell receptor genes of 25 inbred Mus musculus strains and 8 wild Mus species. Included in the inbred mice tested were several strains which spontaneously develop systemic autoimmune disease. Extensive polymorphism was evident for the variable (V) gene segments of the gene family for both the inbred strains and wild mouse species. Changes in the total number of bands hybridizing with probes for V gene segments suggest that members of a V gene segment subfamily are not closely linked, but are interspersed with members of other subfamilies; that expansion and contraction of the multimembered subfamilies may be an important diversifying factor. Our data obtained with gene probes revealed genomic diversity that is much more limited than that seen for the locus. Analysis of inbred mice with probes for the gene locus revealed some RFLPs, but little evidence of expansion or contraction in the numbers of gene segments. Among the autoimmune mice, NZW, NZB, and BXSB/MpJ all display distinctive differences with gene probes. NZW mice have a large deletion of the gene family, which has been reported previously. We found no differences to distinguish the MRL/MpJ lpr/lpr mice from non-autoimmune strains.     

The human T-cell receptor gamma variable pseudogeneV10 is a distinctive marker of human speciation

The nucleotide sequence data reported in this paper have been submitted to the EMBL/GenBank/DDBJ nucleotide sequence databases and have been assigned the accession numbers X86 558 and X86 709–X86 723     

Evolutionary dynamics of the T-cell receptor VB gene family as inferred from the human and mouse genomic sequences

The diversity of T-cell receptors is generated primarily by the variable-region gene families, each of which is composed of a large number of member genes. The entire genomic sequence of the variable region (VB) of the T- cell receptor beta chain from humans and mice has become available. To understand the evolutionary dynamics of the VB gene family, we conducted a phylogenetic analysis of all VB genes from humans and mice, as well as a detailed analysis of internal DNA duplications in the human genomic VB region. The phylogenetic tree obtained shows that human and mouse VB genes intermingle extensively rather than forming two separate clusters and that many gene duplications occurred both before and after the divergence between primates and rodents. Analyzing the genomic maps of transposable elements (e.g., LINEs and SINEs) and relic VB genes in the VB gene region, we present evidence that a 20-kb VB region duplicated tandemly four times in the human lineage during the last 32 Myr, and 6 out of the 15 VB genes in this region have become nonfunctional during this period. Our results show that the VB gene family is subject to evolution by a birth-and-death process rather than to concerted evolution.     

Frequent recombination in the human T-cell receptor beta gene complex

Although individual TCRVBV gene segments exhibit limited polymorphism, human T-cell receptor beta (TCRB) haplotypes are characterized by multiple different combinations of allelic markers. This observation suggests that genetic recombination may have played a role in the generation of these haplotypes. Meiotic recombination in a region spanning 250 kilobases (kb) at the 3 end of the TCRB gene complex was investigated by extended family studies and by analysis of single sperm. Segregation patterns of polymorphic TCRB markers in families allowed the assignment of TCRB alleles to parental haplotypes and detection of recombinants among the offspring. Among the 178 informative paternal meioses, four (2%) were recombinant, whereas no recombinants were found in the 199 maternal meioses. In addition, segregation of two allelic markers was examined in a total of 1101 individual sperm from two heterozygous donors to detect exchange events in this region. The results revealed a similar rate of recombination, 1.3%, which, along with the family data, suggests that at, least in males, meiotic recombination in this 250 kb region may be six times higher than the average rate of 1% per 10⁶ bases that has been estimated for the human genome.     

Comparison of the canine and human olfactory receptor gene repertoires

Background

Olfactory receptors (ORs), the first dedicated molecules with which odorants physically interact to arouse an olfactory sensation, constitute the largest gene family in vertebrates, including around 900 genes in human and 1,500 in the mouse. Whereas dogs, like many other mammals, have a much keener olfactory potential than humans, only 21 canine OR genes have been described to date.

Results

In this study, 817 novel canine OR sequences were identified, and 640 have been characterized. Of the 661 characterized OR sequences, representing half of the canine repertoire, 18% are predicted to be pseudogenes, compared with 63% in human and 20% in mouse. Phylogenetic analysis of 403 canine OR sequences identified 51 families, and radiation-hybrid mapping of 562 showed that they are distributed on 24 dog chromosomes, in 37 distinct regions. Most of these regions constitute clusters of 2 to 124 closely linked genes. The two largest clusters (124 and 109 OR genes) are located on canine chromosomes 18 and 21. They are orthologous to human clusters located on human chromosomes 11q11-q13 and HSA11p15, containing 174 and 115 ORs respectively.

Conclusions

This study shows a strongly conserved genomic distribution of OR genes between dog and human, suggesting that OR genes evolved from a common mammalian ancestral repertoire by successive duplications. In addition, the dog repertoire appears to have expanded relative to that of humans, leading to the emergence of specific canine OR genes.