Tandem repeats modify the structure of the canine CD1D gene

Abstract

SummaryAmong the CD1 proteins that present lipid antigens to T cells, CD1d is the only one that stimulates a population of T cells with an invariant T-cell receptor known as NKT cells. Sequencing of a 722 nucleotide gap in the dog (Canis lupus familiaris) genome revealed that the canine CD1D gene lacks a sequence homologous to exon 2 of human CD1D, coding for the start codon and signal peptide. Also, the canine CD1D gene contains three different short tandem repeats that disrupt the expected gene structure. Because canine CD1D cDNA lacks sequences homologous to human exon 2 and 3, the functionality of canine CD1d protein may be affected, and this could have consequences for the development and activation of canine NKT cells. Keywords CD1, dog, microsatellite, NKT cells, simple sequence repeatThe CD1 family is a group of non-polymorphic glycoproteins that present lipid antigens to T cells (Porcelli & Modlin 1999;Brigl & Brenner 2004;Barral & Brenner 2007). Like MHC class I proteins, CD1 proteins are heterodimers of b2 microglobulin and a heavy chain consisting of three extracellular a domains, a transmembrane region and a cytoplasmic tail, each encoded by a separate exon, preceded by an exon that encodes the start codon and signal peptide, and sometimes an additional exon that consists of 5′ UTR only.Large variation exists in the number of CD1A, CD1B, and CD1C genes between mammalian species, whereas one or two CD1D genes are present in all mammalian species studied to date (Dascher et al. 1999;Hayes & Knight 2001;Eguchi-Ogawa et al. 2007;Looringh van Beeck et al. 2008. CD1d is crucial for the selection (Bendelac et al. 1995) and activation (Kawano et al. 1997) of a subset of T cells known as natural killer T (NKT) cells. The canine CD1 locus is located on chromosome 38 and contains one CD1D gene, eight CD1A genes, one CD1C, one CD1B and one CD1E gene (Fig. 1a) (Looringh van Beeck et al. 2008). In the canine genome (CanFam 3.1) and in the sequence of BAC clone XX-14K12 AC183576.27, the canine CD1D gene is incomplete due to an internal gap of unknown length. Upstream from this gap we detected a sequence with 62% nt identity to exon 1 of human CD1D and downstream from the gap a sequence with 68% identity to human exon 3 (ENST00000368171; www.ensembl.org) (Fig. 1b). No canine homolog of the human CD1D exon 2 was found. Putative full-length canine exons were found for CD1D exon 4, 5, 6 and 7, with identities of respectively 76%, 84%, 58% and 56% to the corresponding human exons.To be able to fill the gap in the genomic DNA sequence between exon 1 and exon 3 of canine CD1D, we performed a two-step digestion on BAC clone XX-14K12 DNA using restriction endonuclease HpaI followed by HindIII and NotI (Fig. S1). The two restriction fragments containing the gap were subsequently cloned and sequenced. The complete DNA sequence of the gap was obtained and consists of 722 nt (GenBank GU930707) (Fig. 1c). No canine homolog of the human CD1D exon 2 was found in this DNA sequence.Using Tandem Repeat Finder, three different types ...

Polymorphisms in the CD1d Promoter That Regulate CD1d Gene Expression Are Associated with Impaired NKT Cell Development

“…Although comparison of the CD1d coding sequences among a number of mammals indicates a relatively high level of evolutionary conservation, recent data suggest the CD1d gene is not fully functional in all species. For example, one recent report indicates that the CD1d gene in dogs lacks exons 2 and 3, and is therefore predicted to be non-functional (44). It has also been reported that many ruminants share a mutation that disrupts the normal CD1d start codon (45–47).…”

In Silicomethod for identification of MHC class I-like molecules in whole genomes

“…The canine locus on the other hand is much larger than the human locus. It has 4 functional CD1a genes and 5 CD1a pseudogenes, and furthermore there is 1 gene of each of the other isoforms [3][4][5] .…”