Analysis of porcine MHC using microarrays
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- 作者：Yu Gao ; Per Wahlberg ; Sylvain Marthey ; Diane Esquerr¨¦ ; Florence Jaffr¨¦zic ; J¨¦rome Lecardonnel ; Karine Hugot ; Claire Rogel-Gaillard
- 关键词：Pig ; MHC ; SLA complex ; Transcriptome ; PBMC ; Immune response ; Stimulation ; Microarrays ; Tiling arrays ; Non coding transcripts ; Annotation
- 刊名：Veterinary Immunology and Immunopathology
- 出版年：2012
- 出版时间：15 July, 2012
- 年：2012
- 卷：148
- 期：1-2
- 页码：78-84
- 全文大小：770 K
文摘
The major histocompatibility complex (MHC) in Mammals is one of the most gene dense regions of the genome and contains the polymorphic histocompatibility gene families known to be involved in pathogen response and control of auto-immunity. The MHC is a complex genetic system that provides an interesting model system to study genome expression regulation and genetic diversity at the megabase scale. The pig MHC or SLA (Swine Leucocyte Antigen) complex spans 2.4 megabases and 151 loci have been annotated. We will review key results from previous RNA expression studies using microarrays containing probes specific to annotated loci within SLA and in addition present novel data obtained using high-density tiling arrays encompassing the whole SLA complex. We have focused on transcriptome modifications of porcine peripheral blood mononuclear cells stimulated with a mixture of phorbol myristate acetate and ionomycin known to activate B and T cell proliferation. Our results show that numerous loci mapping to the SLA complex are affected by the treatment. A general decreased level of expression for class I and II genes and an up-regulation of genes involved in peptide processing and transport were observed. Tiling array-based experiments contributed to refined gene annotations as presented for one SLA class I gene referred to as SLA-11. In conclusion, high-density tiling arrays can serve as an excellent tool to draw comprehensive transcription maps, and improve genome annotations for the SLA complex. We are currently studying their relevance to characterize SLA genetic diversity in combination with high throughput next generation sequencing.