Transcription variants of SLA-7, a swine non classical MHC class I gene

Rui Hu,Gaëtan Lemonnier,Claire Rogel-Gaillard,Emmanuelle Bourneuf,Silvia Vincent-Naulleau

doi:10.1186/1753-6561-5-s4-s10

Abstract

In pig, very little information is available on the non classical class I (Ib) genes of the Major Histocompatibility Complex (MHC) i.e. SLA-6, -7 and -8. Our aim was to focus on the transcription pattern of the SLA-7 gene. RT-PCR experiments were carried out with SLA-7 specific primers targeting either the full coding sequence (CDS) from exon 1 to the 3 prime untranslated region (3UTR) or a partial CDS from exon 4 to the 3UTR. We show that the SLA-7 gene expresses a full length transcript not yet identified that refines annotation of the gene with eight exons instead of seven as initially described from the existing RefSeq RNA. These two RNAs encode molecules that differ in cytoplasmic tail length. In this study, another SLA-7 transcript variant was characterized, which encodes a protein with a shorter alpha 3 domain, as a consequence of a splicing site within exon 4. Surprisingly, a cryptic non canonical GA-AG splicing site is used to generate this transcript variant. An additional SLA-7 variant was also identified in the 3UTR with a splicing site occurring 31 nucleotides downstream to the stop codon. In conclusion, the pig SLA-7 MHC class Ib gene presents a complex transcription pattern with two transcripts encoding various molecules and transcripts that do not alter the CDS and may be subject to post-transcriptional regulation.

Highlights

The Major Histocompatibility Complex (MHC) class I gene family comprises classical (Ia) and non classical (Ib) genes
SLA-7 full coding sequences Full length SLA-7 transcripts were characterized by RTPCR from the thymus of Melanoma-bearing Libechov Minipigs (MeLiM) pigs using the primers SLA-7-e1-F and SLA-7-3 prime untranslated region (3UTR)-R (Table 1 and Figure 1)
The SLA-7-001 encoded protein contains a cytoplasmic tail that is defined by exons 6 and 7 and is 68 aminoacids long

Summary

Introduction

The Major Histocompatibility Complex (MHC) class I gene family comprises classical (Ia) and non classical (Ib) genes. The highly polymorphic class Ia genes are widely expressed and encode membrane-bound glycoproteins that present self and viral peptides to cytotoxic T cells [1] and modulate the activity of natural killer cells [2]. The class Ib genes display limited polymorphism, and are predominantly expressed in immunotolerant organ sites in human, notably at the feto-maternal interface [3]. Three MHC class Ib genes have been characterized, namely HLA-E, -F and -G[3] and HLA-G has been shown to express alternatively spliced variants encoding various membranebound as well as soluble proteins [4]. The H2QaI gene is orthologous to HLA-E[5] and functional homologies have been established between H2-Qa2 and HLA-G[6]. One to four MHC class Ib genes have been

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