Kulski J K, Dunn D S
Centre for Bioinformatics and Biological Computing, School of Information Technology, Murdoch University, Murdoch, Western Australia.
Cytogenet Genome Res. 2005;110(1-4):193-202. doi: 10.1159/000084952.
Most polymorphic Alu insertions (POALINs) belong to a subgroup of the Alu multicopy retrotransposon family of short interspersed nucleotide elements (SINEs) that are categorized as AluYb8 and AluYa5. The number of AluYb8/AluYa5 members (approximately 4,492 copies) is significantly less than the approximately one million fixed Alu copies per human genome. We have studied the presence of POALINs within the Major Histocompatibility Complex (MHC) class I region on the short arm of chromosome 6 (6p21.3) because this region has a high gene density, many genes with immune system functions, large sequence variations and diversity, duplications and redundancy, and a strong association with more than 100 different diseases. Since little is known about POALINs within the MHC genomic region, we undertook to identify some of the members of the AluYb8/AluYa5 subfamily and to study their frequency of distribution and genetic characteristics in different populations. As a result of our comparative genomic analyses, we identified the insertion sites for five POALINs distributed within the MHC class I region. This brief review outlines the locations of the insertions and sequence features of the five MHC POALINs, their single site and haplotype frequencies in different geographic populations, and their association with different HLA class I genes and disease. We show that the MHC POALINs have a potential value as lineage and linkage markers for the study of human population genetics, disease associations, genomic diversity and evolution.
大多数多态性Alu插入序列（POALINs）属于短散在核元件（SINEs）的Alu多拷贝逆转录转座子家族的一个亚组，被归类为AluYb8和AluYa5。AluYb8/AluYa5成员的数量（约4492个拷贝）明显少于人类基因组中约一百万个固定的Alu拷贝。我们研究了6号染色体短臂（6p21.3）上主要组织相容性复合体（MHC）I类区域内POALINs的存在情况，因为该区域具有高基因密度、许多具有免疫系统功能的基因、大的序列变异和多样性、重复和冗余，并且与100多种不同疾病有很强的关联。由于对MHC基因组区域内的POALINs了解甚少，我们着手鉴定AluYb8/AluYa5亚家族的一些成员，并研究它们在不同人群中的分布频率和遗传特征。通过我们的比较基因组分析，我们确定了分布在MHC I类区域内的五个POALINs的插入位点。这篇简短的综述概述了五个MHC POALINs的插入位置和序列特征、它们在不同地理人群中的单一位点和单倍型频率，以及它们与不同HLA I类基因和疾病的关联。我们表明，MHC POALINs作为谱系和连锁标记，在人类群体遗传学、疾病关联、基因组多样性和进化研究中具有潜在价值。
