Genetic variation of MHC Class I polymorphic Alu insertions (POALINs) in three sub-populations of the East Midlands, UK

BACKGROUND

Alu elements are highly researched due to their useful nature as markers in the study of human population genetics. Recently discovered Major Histocompatibility Complex (MHC) polymorphic Alu insertions (POALINs) have not been examined extensively for genetic variation and their HLA associations.

AIMS

The aim of this study is to assess the genetic variation between three populations using five recently discovered POALINs.

METHODS AND SUBJECTS

The study examined 190 healthy, unrelated subjects from three different populations in the East Midlands (UK) for the presence or absence of five Alu elements (AluHG, AluMICB, AluHJ, AluTF and AluHF) via the polymerase chain reaction followed by gel electrophoresis. Data were analysed for genetic variation and phylogenetic analyses.

RESULTS

All Alus were polymorphic in study populations. Appreciable allele frequency variation was observed at a number of loci. The British population was significantly different from both the Punjabi Jat Sikh and Gujarati Patel populations, although showing a closer genetic relationship to the Punjabi Jat Sikh population than the Gujarati Patel population (Nei's D_A = 0.0031 and 0.0064, respectively).

CONCLUSIONS

MHC POALINs are useful markers in the investigation of genetic variation and the assessment of population relationships, and may have some bearing on disease associations due to their linkage disequilibrium with HLA loci; this warrants further studies.

Polymorphic Alu insertions among Mayan populations

The Mayan homeland within Mesoamerica spans five countries: Belize, El Salvador, Guatemala, Honduras and Mexico. There are indications that the people we call the Maya migrated from the north to the highlands of Guatemala as early as 4000 B.C. Their existence was village-based and agricultural. The culture of these Preclassic Mayans owes much to the earlier Olmec civilization, which flourished in the southern portion of North America. In this study, four different Mayan groups were examined to assess their genetic variability. Ten polymorphic Alu insertion (PAI) loci were employed to ascertain the genetic affinities among these Mayan groups. North American, African, European and Asian populations were also examined as reference populations. Our results suggest that the Mayan groups examined in this study are not genetically homogeneous.

Polymorphic Alu insertions within the Major Histocompatibility Complex class I genomic region: a brief review

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.

On the distribution and genetic differentiation of Anopheles gambiae s.s. molecular forms

This paper summarises published and unpublished data on the spatial and temporal distribution, and on the genetic characterisation of molecular forms M and S of Anopheles gambiae s.s. The two forms are characterised by a high level of gene-flow restriction, by a largely overlapping geographical and temporal distribution, and by a low degree of genetic differentiation. Floating paracentric inversions on chromosome-2 are shown to be shared by the two forms, although with very different frequencies of alternative arrangements, confirming that these inversions are most probably involved in ecotypic adaptation, rather than in the building of reproductive barriers. Further studies and tools are needed to throw light on the genetic and biological differentiation of M and S to improve the knowledge of the real composition of the vector system, of its demography, population genetics and dynamics, also in view of the possible consequences on the transmission of human pathogens in sub-Saharan Africa. Preliminary results and perspectives of the use of transposable element insertion sites as markers of genetic differentiation and tools for population genetic studies are discussed.

Phylogenetic information in polymorphic L1 andAlu insertions from East Asians and Native American populations

This study attempts to ascertain genetic affinities between Native American and East Asian populations by analyzing four polymorphic Alu insertions (PAIs) and three L1 polymorphic loci. These two genetic systems demonstrated strong congruence when levels of diversity and genetic distances were considered. Overall, genetic relatedness within Native American groups does not correlate with geographical and linguistic structure, although strong grouping for Native Americans with East Asians was demonstrated, with clear discrimination from African and European groups. Most of the variation was assigned to differences occurring within groups, but the interpopulation variation found for South Amerindians was recognizably higher in comparison to the other sampled groups of populations. Our data suggest that bottleneck events followed by strong influence of genetic drift in the process of the peopling of the Americas may have been determinant factors in delineating the genetic background of present-day South Amerindians. Since no clear subgroups were detected within Native Americans and East Asians, there is no indication of multiple waves in the early colonization of the New World.

Mosquito transposable elements

The completion of the genome assembly for the African malaria mosquito, Anopheles gambiae, and continuing genomic efforts for the yellow fever mosquito, Aedes aegypti, have allowed the use of bioinformatics tools to identify and characterize a diverse array of transposable elements (TEs) in these and other mosquito genomes. An overview of the types and number of both RNA-mediated and DNA-mediated TEs that are found in mosquito genomes is presented. A number of novel and interesting TEs from these species are discussed in more detail. These findings have significant implications for our understanding of mosquito genome evolution and for future modifications of natural mosquito populations through the use of TE-mediated genetic transformation.

Molecular variability in Amerindians: widespread but uneven information

A review was made in relation to the molecular variability present in North, Central, and South American Indian populations. It involved results from ancient DNA, mitochondrial DNA in extant populations, HLA and other autosomal markers, X and Y chromosome variation, as well as data from parasitic viruses which could show coevolutionary changes. The questions considered were their origin, ways in which the early colonization of the continent took place, types and levels of the variability which developed, peculiarities of the Amerindian evolutionary processes, and eventual genetic heterogeneity which evolved in different geographical areas. Although much information is already available, it is highly heterogeneous in relation to populations and types of genetic systems investigated. Unfortunately, the present trend of favoring essentially applied research suggest that the situation will not basically improve in the future.