Nucleotide Sequencing Analysis of the 146-Kilobase Segment around theIkBLandMICAGenes at the Centromeric End of the HLA Class I Region

Shiina, Takashi; Tamiya, Gen; Oka, Akira; Yamagata, Tetsushi; Yamagata, Naomi; Kikkawa, Eri; Goto, Kaori; Mizuki, Nobuhisa; Watanabe, Kôji; Fukuzumi, Yasuhito; Taguchi, Susumu; Sugawara, Chiyo; Ono, Ayako; Chen, Lei; Yamazaki, Masaaki; Tashiro, Hiroyuki; Andõ, Akira; Ikemura, Toshimichi; Kimura, Minoru; Inoko, Hidetoshi

doi:10.1006/geno.1997.5114

Cited by 79 publications

(63 citation statements)

References 57 publications

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“…The human MHC-B and MHC-C were generated by GFD in evolution (24)(25)(26)(27)(28). This GFD was also confirmed by the genome sequencing of the whole human MHC gene complex (21).…”

Section: Origin Of Mhc-b and Mhc-cmentioning

confidence: 85%

Genomic evolution of MHC class I region in primates

Fukami-Kobayashi

Shiina

Anzai

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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To elucidate the origins of the MHC-B-MHC-C pair and the MHC class I chain-related molecule (MIC)A-MICB pair, we sequenced an MHC class I genomic region of humans, chimpanzees, and rhesus monkeys and analyzed the regions from an evolutionary stand-point, focusing first on LINE sequences that are paralogous within each of the first two species and orthologous between them. Because all the long interspersed nuclear element (LINE) sequences were fragmented and nonfunctional, they were suitable for conducting phylogenetic study and, in particular, for estimating evolutionary time. Our study has revealed that MHC-B and MHC-C duplicated 22.3 million years (Myr) ago, and the ape MICA and MICB duplicated 14.1 Myr ago. We then estimated the divergence time of the rhesus monkey by using other orthologous LINE sequences in the class I regions of the three primate species. The result indicates that rhesus monkeys, and possibly the Old World monkeys in general, diverged from humans 27-30 Myr ago. Interestingly, rhesus monkeys were found to have not the pair of MHC-B and MHC-C but many repeated genes similar to MHC-B. These results support our inference that MHC-B and MHC-C duplicated after the divergence between apes and Old World monkeys

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“…The human MHC-B and MHC-C were generated by GFD in evolution (24)(25)(26)(27)(28). This GFD was also confirmed by the genome sequencing of the whole human MHC gene complex (21).…”

Section: Origin Of Mhc-b and Mhc-cmentioning

confidence: 85%

Genomic evolution of MHC class I region in primates

Fukami-Kobayashi

Shiina

Anzai

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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“…This finding is consistent with previous hypotheses that there has been very little recombination between the HLA-B and MICA loci during the successive duplications that engender the present HLA class I region. 29,30 It is worth noting that LD also varied within this genomic region in a haplotype-specific manner. Strong LD was found across populations in HLA-B*1503-MICA*00801 haplotype while confined to certain populations in several haplotypes.…”

Section: Discussionmentioning

confidence: 99%

MICA, HLA-B haplotypic variation in five population groups of sub-Saharan African ancestry

Tian

et al. 2003

Genes Immun

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The human major histocompatibility complex (MHC) class I chain-related gene A (MICA), located 46 kb centromeric to HLA-B, encodes a stress-inducible protein, which is a ligand for the NKG2D receptor. In addition to its primary role in immune surveillance, data suggest that MICA is involved in the immune response to transplants and in susceptibility to some diseases. In this study, 152 subjects from the Yoruba (n¼74), Efik (n¼32), and Igbo (n¼46) tribes of southern Nigeria, 39 nationwide African-American stem cell donors, and 60 African-American individuals residing in the metropolitan Boston area were studied for MICA, HLA-B allelic variation, haplotypic diversity, and linkage disequilibrium (LD). MICA and HLA-B exhibited a high degree of genetic diversity among the populations studied. In particular, MICA allele and HLA-B-MICA haplotype frequencies and LD in the Efik and Igbo tribes were significantly different from the other study groups. HLA-B and MICA loci demonstrated significant global LD in all five populations (P-values o0.00001). LD also varied in a haplotype-specific manner. A novel MICA allele was detected in the Boston population. These findings are important from an anthropologic perspective, and will inform future HLA-linked disease association studies in related ethnic groups of African-derived ancestry.

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“…BAC clones 205N13, 62H24, 195P8, 88K6, 246G18, 41G14, and 211G14 were subjected to nucleotide sequence determination by combination of massively parallel pyrosequencing (15) and/or bidirectional shotgun sequencing (16).…”

Section: Nucleotide Sequencingmentioning

confidence: 99%

Genomic Sequence Analysis of the MHC Class I G/F Segment in Common Marmoset (Callithrix jacchus)

Kono

Brameier

Roos

et al. 2014

The Journal of Immunology

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The common marmoset (Callithrix jacchus) is a New World monkey that is used frequently as a model for various human diseases. However, detailed knowledge about the MHC is still lacking. In this study, we sequenced and annotated a total of 854 kb of the common marmoset MHC region that corresponds to the HLA-A/G/F segment (Caja-G/F) between the Caja-G1 and RNF39 genes. The sequenced region contains 19 MHC class I genes, of which 14 are of the MHC-G (Caja-G) type, and 5 are of the MHC-F (Caja-F) type. Six putatively functional Caja-G and Caja-F genes (Caja-G1, Caja-G3, Caja-G7, Caja-G12, Caja-G13, and Caja-F4), 13 pseudogenes related either to Caja-G or Caja-F, three non-MHC genes (ZNRD1, PPPIR11, and RNF39), two miscRNA genes (ZNRD1-AS1 and HCG8), and one non-MHC pseudogene (ETF1P1) were identified. Phylogenetic analysis suggests segmental duplications of units consisting of basically five (four Caja-G and one Caja-F) MHC class I genes, with subsequent expansion/deletion of genes. A similar genomic organization of the Caja-G/F segment has not been observed in catarrhine primates, indicating that this genomic segment was formed in New World monkeys after the split of New World and Old World monkeys.

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Nucleotide Sequencing Analysis of the 146-Kilobase Segment around theIkBLandMICAGenes at the Centromeric End of the HLA Class I Region

Cited by 79 publications

References 57 publications

Genomic evolution of MHC class I region in primates

Genomic evolution of MHC class I region in primates

MICA, HLA-B haplotypic variation in five population groups of sub-Saharan African ancestry

Genomic Sequence Analysis of the MHC Class I G/F Segment in Common Marmoset (Callithrix jacchus)

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