Polymorphic SVA retrotransposons at four loci and their association with classical HLA class I alleles in Japanese, Caucasians and African Americans

Kulski, Jerzy K.; Shigenari, Atsuko; Inoko, Hidetoshi

doi:10.1007/s00251-010-0427-2

Cited by 9 publications

(29 citation statements)

References 42 publications

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“…UTR were listed for informative purposes as the network is based on protein sequences. The resulting network revealed an HLA-A clustering in accordance with other studies [45], [46], [47]. The five HLA-A lineages previously defined by Gu et al [45] are also indicated.…”

Section: Resultssupporting

confidence: 88%

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HLA-G UTR Haplotype Conservation in the Malian Population: Association with Soluble HLA-G

et al. 2013

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The HLA-G molecule plays an important role in immunomodulation. In a previous study carried out on a southern French population our team showed that HLA-G haplotypes, defined by SNPs in the coding region and specific SNPs located in 5′URR and 3′UTR regulatory regions, are associated with differential soluble HLA-G expression (sHLA-G). Furthermore, the structure of these HLA-G haplotypes appears to be conserved in geographically distant populations.The aim of our study is to confirm these expectations in a sub-Saharan African population and to explore additional factors, such as HLA-A alleles, that might influence sHLA-G expression.DNA and plasma samples were collected from 229 Malians; HLA-G and HLA-A genotyping were respectively performed by the Snap Shot® method and by Luminex™ technology. sHLA-G dosage was performed using an ELISA kit. HLA-G and HLA-A allelic and haplotypic frequencies were estimated using an EM algorithm from the Gene[Rate] program. Associations between genetic and non genetic parameters with sHLA-G were performed using a non-parametric test with GRAPH PAD Prism 5.Our results reveal a good conservation of the HLA-G UTR haplotype structure in populations with different origins and demographic histories. These UTR haplotypes appear to be involved in different sHLA-G expression patterns. Specifically, the UTR-2 haplotype was associated with low sHLA-G levels, displaying a dominant negative effect. Furthermore, an allelic effect of both HLA-G and HLA-A, as well as non genetic parameters, such as age and gender possibly linked to osteogenesis and sexual hormones, also seem to be involved in the modulation of sHLA-G.These data suggest that further investigation in larger cohorts and in populations from various ethnical backgrounds is necessary not only to detect new functional polymorphism in HLA-G regulatory regions, but also to reveal the extent of biological phenomena that influence sHLA-G secretion and this might therefore have an impact on transplantation practice.

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Section: Resultssupporting

confidence: 88%

“…In order to establish the relationships among the HLA-A and HLA-G haplotypes, a Median Joining (MJ) network [44] based on protein sequences was constructed using the program Network (www.fluxus-engineering.com/network). The HLA-A alleles were grouped into five lineages previously defined [45], [46], [47].…”

Section: Methodsmentioning

confidence: 99%

HLA-G UTR Haplotype Conservation in the Malian Population: Association with Soluble HLA-G

et al. 2013

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“…The frequency of this presence or absence of specific SVAs located in HLA genes has shown to be variable between groups with different ethnic origins [53]. This demonstrates the variability of SVA insertions between individuals; our study extends the analysis of their polymorphic nature to include the variation found in the CCCTCT hexamer repeat and provides further evidence of the already characterised variation in the second domain of the central VNTR (Table 2).…”

Section: Discussionsupporting

confidence: 68%

Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns

et al. 2013

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BackgroundRetrotransposons are a major component of the human genome constituting as much as 45%. The hominid specific SINE-VNTR-Alus are the youngest of these elements constituting 0.13% of the genome; they are therefore a practical and amenable group for analysis of both their global integration, polymorphic variation and their potential contribution to modulation of genome regulation.ResultsConsistent with insertion into active chromatin we have determined that SVAs are more prevalent in genic regions compared to gene deserts. The consequence of which, is that their integration has greater potential to have affects on gene regulation. The sequences of SVAs show potential for the formation of secondary structure including G-quadruplex DNA. We have shown that the human specific SVA subtypes (E-F1) show the greatest potential for forming G-quadruplexes within the central tandem repeat component in addition to the 5’ ‘CCCTCT’ hexamer. We undertook a detailed analysis of the PARK7 SVA D, located in the promoter of the PARK7 gene (also termed DJ-1), in a HapMap cohort where we identified 2 variable number tandem repeat domains and 1 tandem repeat within this SVA with the 5’ CCCTCT element being one of the variable regions. Functionally we were able to demonstrate that this SVA contains multiple regulatory elements that support reporter gene expression in vitro and further show these elements exhibit orientation dependency.ConclusionsOur data supports the hypothesis that SVAs integrate preferentially in to open chromatin where they could modify the existing transcriptional regulatory domains or alter expression patterns by a variety of mechanisms.

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“…These class II and OR‐POALINs would be an useful addition to the class I POALINs for future population studies because the more the Alu loci are used in a comparison of populations, the better the average consensus plot will be for discerning the interrelation of different populations and providing a clearer picture of POALIN and HLA relationships between populations. Apart from the polymorphic Alu insertions within the HLA genomic region, there are other dimorphic retrotransposons such as SVA, L1 (Kulski, Shigenari, & Inoko, ), LTR (Kulski et al, ) and HERVs (Kulski et al, ) that also could be used in population MHC genetic diversity studies. Furthermore, sequencing these MHC class I and II Alu insertions by the Sanger method or next‐generation sequencing to detect SNPs within their aligned sequences could provide an additional useful layer of analysis within and between populations as was previously shown for the solitary LTR indel MER9 in the HLA class I alpha block (Kulski et al, ).…”

Section: Resultsmentioning

confidence: 99%

MHC class I polymorphic Alu insertion (POALIN) allele and haplotype frequencies in the Arabs of the United Arab Emirates and other world populations

Kulski

Mawart

Marie

et al. 2019

Int J Immunogenetics

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Polymorphic Alu insertions (POALINs) are found throughout the human genome and have been used in various studies to infer geographic origin of human populations. The main aim of this study was to determine the allele and haplotype frequencies of five POALINs, AluHF, AluHG, AluHJ, AluTF and AluMICB, within the major histocompatibility complex (MHC) class I region of 95 UAE Arabs, and correlate their frequencies to those of the HLA‐A, HLA‐C and HLA‐B class I allele lineages. Evolutionary relationships between the POALINs of the Arabs and those previously studied in populations of African, Asian and European descent were compared. At each of the five Alu loci (AluHF, AluHG, AluHJ, AluTF and AluMICB), Alu insertion was designated as Alu(locus)*02 and absence was Alu(locus)*01. The AluHG insertion (AluHG*02) had the highest frequency (0.332), followed by AluHF*02 (0.300), AluHJ*02 (0.263), AluMICB*02 (0.111) and AluTF*02 (0.058). Of the 270 Alu‐HLA haplotypes pairs in the UAE Arabs, 110 had no Alu insertion, and 54 had an Alu insertion at >50% per haplotype. An Alu insertion >75% per haplotype was found between AluMICB*02 and HLA‐B*14, HLA‐B*22, HLA‐B*44, HLA‐B*55, HLA‐B*57 and HLA‐B*73, and with HLA‐C*01 and HLA‐C*18; AluHJ*02 with HLA‐A*01, HLA‐A*19, HLA‐A*24 and HLA‐A*32; AluHG*02 with HLA‐A*02 and HLA‐B*18; and AluHF*02 with HLA‐A*10. The genotyped allele and haplotype frequencies of the MHC POALINs in UAE Arabs were compared with the results of 30 previously published Asian, European, American and African populations. Phylogenetic and multidimensional scaling (MDS) analysis of the relative MHC POALINs allele and haplotype frequencies revealed that the UAE Arabs have a similar lineage to Caucasians and the most distant genetic relationship to the Waorani native American population of Ecuador. The structure of both the phylogenetic tree and the MDS analysis supports the Out of Africa theory of human evolution. The nature of the clusters suggests the Arabian Middle East represents a crossroads from which human populations migrated towards Asia in the east and Europe to the north‐west.

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Polymorphic SVA retrotransposons at four loci and their association with classical HLA class I alleles in Japanese, Caucasians and African Americans

Cited by 9 publications

References 42 publications

HLA-G UTR Haplotype Conservation in the Malian Population: Association with Soluble HLA-G

HLA-G UTR Haplotype Conservation in the Malian Population: Association with Soluble HLA-G

Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns

MHC class I polymorphic Alu insertion (POALIN) allele and haplotype frequencies in the Arabs of the United Arab Emirates and other world populations

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