IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations

Abstract

Background: Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract.Description: IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the αβ and γδ TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the αβ TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(D)J genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at http://imgt.cines.fr/ GeneInfo. Conclusion:IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis.

IMGT Unique Numbering for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSF

“…The IMGT unique numbering is used (i) for the annotation of sequences, genes, and structures in the IMGT databases: IMGT/LIGM-DB , IMGT/CLL-DB (Brochet 2008), IMGT/ GENE-DB (Giudicelli et al 2005), IMGT/2Dstructure-DB and IMGT/3Dstructure-DB Ehrenmann et al 2010b), (ii) for the analysis of sequences and structures in the IMGT online tools: IMGT/V-QUEST Brochet et al 2008;Giudicelli and Lefranc 2009), IMGT/JunctionAnalysis (Yousfi Monod et al 2004;Bleakley et al 2006), IMGT/HighV-QUEST (Alamyar et al 2010), IMGT/Phylogene (Elemento and Lefranc 2003), IMGT/GeneInfo (Baum et al 2004(Baum et al , 2006, IMGT/LIGMotif (Lane et al 2010), IMGT/DomainGapAlign, IMGT/DomainDisplay and IMGT/Collier de Perles (Ehrenmann et al 2010b), and (iii) in the data management of the IMGT knowledge web resources: IMGT Protein displays, IMGT Alignments of alleles, IMGT As a major IMGT-ONTOLOGY concept of numerotation, the IMGT unique numbering is used, with the IMGT-ONTOLOGY concepts of classification (From IMGT-ONTOLOGY CLASSIFICATION Axiom to IMGT Standardized Gene and Allele Nomenclature: For Immunoglobulins (IG) and T Cell Receptors (TR) [Lefranc 2011d]) and concepts of description (From IMGT-ONTOLOGY DESCRIPTION Axiom to…”

IMGT, the International ImMunoGeneTics Information System

“…They allow one to view genes in a locus (IMGT/GeneView, IMGT/LocusView), to search for clones (IMGT/CloneSearch), to search for genes in a locus based on IMGT gene names, functionality, or localization on the chromosome (IMGT/GeneSearch, IMGT/GeneInfo) (Baum et al 2004(Baum et al , 2006, to identify and describe IG and TR genes in large genomic sequences (IMGT/LIGMotif) (Lane et al 2010), or to provide a graphical representation of the numbers of available sequences containing rearranged IG and TR genes (IMGT/ GeneFrequency).…”

Biology of porcine T lymphocytes

“…In humans, a and b chains of ab TCR contain approximately 70 and 52 variable (V) gene segments, 0 and 2 diversity (D) gene segments, and 61 and 13 joining (J) gene segments, respectively (Rowen et al, 1996). Human g and d chains of gd TCR contain only 6 and 3 V gene segments, 0 and 3 D gene segments, and 5 and 4 J gene segments, respectively (Baum et al, 2006). These gene segments rearrange with great (for ab TCR) or limited (for gd TCR) numbers of combination to form TCR V region.…”

“…These gene segments rearrange with great (for ab TCR) or limited (for gd TCR) numbers of combination to form TCR V region. The resulting V regions of ab TCR have approximately 10 18 different antigen specificities, while the V region of gd TCR contains far less antigenic diversity (Rowen et al, 1996;Baum et al, 2006). In pigs, polymerase chain reaction analysis of the complementarity-determining region 3 (CDR3) of the TCR d chain suggests that the V region of the gd TCR is polyclonal in young pigs and becomes oligoclonal with age (Holtmeier et al, 2002).…”