Nucleotide Sequence Analysis of the HLA Class I Region Spanning the 237-kb Segment around the HLA-B and -C Genes

Mizuki, Nobuhisa; Ando, Hitoshi; Kimura, Minoru; Ohno, Shigeaki; Miyata, Shoji; Yamazaki, Masaaki; Tashiro, Hiroyuki; Watanabe, Kôji; Ono, Ayako; Taguchi, Susumu; Sugawara, Chiyo; Fukuzumi, Yasuhito; Okumura, Katsuhiko; Goto, Kaori; Ishihara, Mami; Nakamura, Satoshi; Yonemoto, Junichi; Kikuti, Yara Yukie; Shiina, Takashi; Chen, Lei; Andõ, Akira; Ikemura, Toshimichi; Inoko, Hidetoshi

doi:10.1006/geno.1997.4708

Cited by 99 publications

(73 citation statements)

References 23 publications

(9 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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: 83%

Genomic evolution of MHC class I region in primates

Fukami-Kobayashi

Shiina

Anzai

et al. 2005

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

Self Cite

View full text Add to dashboard Cite

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

show abstract

“…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: 83%

Genomic evolution of MHC class I region in primates

Fukami-Kobayashi

Shiina

Anzai

et al. 2005

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

Self Cite

View full text Add to dashboard Cite

show abstract

“…Three BAC clones and two long-PCR products that covered 242 kb from the BG3 to CD1A1 genes were completely and bidirectionally shotgun sequenced with an average redundancy of 7.5, which was sufficient for assembly and analysis of the entire sequence using previously established procedures (26,27). The completed sequence was compared with previously published chicken genomic sequences from the B12 haplotype found in GenBank accession nos.…”

Section: Dna Sequencing and Analysismentioning

confidence: 99%

Extended Gene Map Reveals Tripartite Motif, C-Type Lectin, and Ig Superfamily Type Genes within a Subregion of the Chicken MHC-B Affecting Infectious Disease

Shiina

Briles

Goto

et al. 2007

The Journal of Immunology

Self Cite

115

149

View full text Add to dashboard Cite

MHC haplotypes have a remarkable influence on whether tumors form following infection of chickens with oncogenic Marek’s disease herpesvirus. Although resistance to tumor formation has been mapped to a subregion of the chicken MHC-B region, the gene or genes responsible have not been identified. A full gene map of the subregion has been lacking. We have expanded the MHC-B region gene map beyond the 92-kb core previously reported for another haplotype revealing the presence of 46 genes within 242 kb in the Red Jungle Fowl haplotype. Even though MHC-B is structured differently, many of the newly revealed genes are related to loci typical of the MHC in other species. Other MHC-B loci are homologs of genes found within MHC paralogous regions (regions thought to be derived from ancient duplications of a primordial immune defense complex where genes have undergone differential silencing over evolutionary time) on other chromosomes. Still others are similar to genes that define the NK complex in mammals. Many of the newly mapped genes display allelic variability and fall within the MHC-B subregion previously shown to affect the formation of Marek’s disease tumors and hence are candidates for genes conferring resistance.

show abstract

“…Fourteen chimpanzee BAC clones that covered Ϸ1.75 Mb from the LTB to Patr-F genes were completely and bidirectionally shotgun sequenced with an average redundancy of 7.0ϫ, which was sufficient for assembly and analysis of the entire sequence using previously established procedures (10,20). The chimpanzee sequence was compared with our previously published human sequence (GenBank accession nos.…”

Section: Bacterialmentioning

confidence: 99%

“…The chimpanzee sequence was compared with our previously published human sequence (GenBank accession nos. AP000502-000521) (10,20). Sequence alignments were performed and homologies determined by using the programs contained within the GENETYX Ver.…”

Section: Bacterialmentioning

confidence: 99%

Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence

Anzai

Shiina²,

Kimura³

et al. 2003

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

Self Cite

117

108

View full text Add to dashboard Cite

Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (Ϸ6 million years ago), the molecular basis of traits unique to humans vs. their closest relative, the chimpanzee, is largely unknown. This report describes a large-scale single-contig comparison between human and chimpanzee genomes via the sequence analysis of almost one-half of the immunologically critical MHC. This 1,750,601-bp stretch of DNA, which encompasses the entire class I along with the telomeric part of the MHC class III regions, corresponds to an orthologous 1,870,955 bp of the human HLA region. Sequence analysis confirms the existence of a high degree of sequence similarity between the two species. However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions͞deletions (indels) dispersed throughout the region. This is functionally exemplified by a large deletion of 95 kb between the virtual locations of human MICA and MICB genes, which results in a single hybrid chimpanzee MIC gene, in a segment of the MHC genetically linked to species-specific handling of several viral infections (HIV͞SIV, hepatitis B and C) as well as susceptibility to various autoimmune diseases. Finally, if generalized, these data suggest that evolution may have used the mechanistically more drastic indels instead of the more subtle singlenucleotide substitutions for shaping the recently emerged primate species.

show abstract

Nucleotide Sequence Analysis of the HLA Class I Region Spanning the 237-kb Segment around the HLA-B and -C Genes

Cited by 99 publications

References 23 publications

Genomic evolution of MHC class I region in primates

Genomic evolution of MHC class I region in primates

Extended Gene Map Reveals Tripartite Motif, C-Type Lectin, and Ig Superfamily Type Genes within a Subregion of the Chicken MHC-B Affecting Infectious Disease

Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence

Contact Info

Product

Resources

About