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Sequence features of HLA-DRB1 locus define putative basis for gene conversion and point mutations
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology. (Kukkonen)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology. (Kukkonen)
2008 (English)In: BMC Genomics, ISSN 1471-2164, Vol. 9, 228- p.Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: HLA/MHC class II molecules show high degree of polymorphism in the human population. The individual polymorphic motifs have been suggested to be propagated and mixed by transfer of genetic material (recombination, gene conversion) between alleles, but no clear molecular basis for this has been identified as yet. A large number of MHC class II allele sequences is publicly available and could be used to analyze the sequence features behind the recombination, revealing possible basis for such recombination processes both in HLA class II genes and other genes, which recombination acts upon. RESULTS: In this study we analyzed the vast dataset of human allelic variants (49 full coding sequences, 374 full exon 2 sequences) of the most polymorphic MHC class II locus, HLA-DRB1, and identified many previously unknown sequence features possibly contributing to the recombination. The CpG-dinucleotide content of exon 2 (containing the antigen-binding sites and subsequently a high degree of polymorphism) was much elevated as compared to the other exons despite similar overall G+C content. Furthermore, the CpG pattern was highly conserved. We also identified more complex, highly conserved sequence motifs in exon 2. Some of these can be identified as putative recombination motifs previously found in other genes, but most are previously unidentified. CONCLUSION: The identified sequence features could putatively act in recombination allowing either less (CpG dinucleotides) or more specific DNA cleavage (complex sequences) or homologous recombination (complex sequences).

Place, publisher, year, edition, pages
2008. Vol. 9, 228- p.
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-16897DOI: 10.1186/1471-2164-9-228ISI: 000256400200002PubMedID: 18489735OAI: oai:DiVA.org:uu-16897DiVA: diva2:44668
Available from: 2008-06-09 Created: 2008-06-09 Last updated: 2009-11-03Bibliographically approved

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