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Human Molecular Genetics Advance Access originally published online on October 19, 2005
Human Molecular Genetics 2005 14(23):3619-3628; doi:10.1093/hmg/ddi389
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Evidence of balancing selection at the HLA-G promoter region

Zheng Tan*, Andrew Minsoo Shon and Carole Ober

Department of Human Genetics, The University of Chicago, Chicago, IL, USA

* To whom correspondence should be addressed at: Department of Human Genetics, The University of Chicago, 920 East 58th Street, Room 501, Chicago, IL 60637, USA. Tel: +1 7737025898; Fax: +1 7738340505; Email: tzheng{at}genetics.uchicago.edu

Received August 15, 2005; Accepted October 12, 2005

HLA-G is a class Ib HLA gene with unique tissue expression pattern and immunomodulatory properties. Polymorphisms in the HLA-G promoter region have been associated with miscarriage and asthma, whereas expression levels have been associated with a wide range of pathologic conditions as well as survival of embryos after in vitro fertilization and of organs after transplantation. Here, we characterize the sequence variation and haplotype structure of the HLA-G promoter and flanking sequences in 44 African Americans, 47 European Americans and 43 Han Chinese by haplotype-specific PCR and sequencing. In all three populations, we observed high levels of nucleotide variation, an excess of intermediate-frequency alleles, and a genealogy with two common haplotypes separated by deep branches, features that are suggestive of balancing selection acting in this region. Comparisons to HLA-A and a pseudogene, HLA-J, suggested that the observed pattern of sequence variation in the HLA-G promoter region is not likely due to other selected HLA genes. We suggest that the mechanism for this selection is related to the highly regulated expression pattern of HLA-G and that high- and low-expressing promoters may be favored under temporally and/or spatially varying selective pressures.


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