Genomic Evolution of MHC Class I Region in Primates

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 standpoint, focusing first on LINE sequences that are para...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 102; no. 26; pp. 9230 - 9234
Main Authors Fukami-Kobayashi, Kaoru, Shiina, Takashi, Anzai, Tatsuya, Sano, Kazumi, Yamazaki, Masaaki, Inoko, Hidetoshi, Tateno, Yoshio, Ohta, Tomoko
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 28.06.2005
National Acad Sciences
Subjects
Animals
Apes
Biological Sciences
Chimpanzees
Divergent evolution
Evolution
Evolution, Molecular
Genes, MHC Class I - genetics
Genome
Genomes
Genomics
Histocompatibility Antigens Class I - genetics
HLA-B Antigens - genetics
HLA-C Antigens - genetics
Humans
Long Interspersed Nucleotide Elements
Macaca mulatta
Mica
Molecules
Monkeys
Pan troglodytes
Primates
Protein Structure, Tertiary
Regional identity
Time Factors
Online AccessGet full text
ISSN0027-8424
1091-6490
1091-6490
DOI10.1073/pnas.0500770102

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Abstract 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 standpoint, 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.
AbstractList 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.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.
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.
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. long interspersed nuclear element (LINE) MHC class I chain-related molecule genomic evolution primate evolution
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 standpoint, 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.
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. [PUBLICATION ABSTRACT]
Author Sano, Kazumi
Fukami-Kobayashi, Kaoru
Anzai, Tatsuya
Yamazaki, Masaaki
Tateno, Yoshio
Shiina, Takashi
Ohta, Tomoko
Inoko, Hidetoshi
AuthorAffiliation RIKEN BioResource Center, RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan; † Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; ‡ BioScience Research Laboratory, Fujiya Co., Ltd., Hadano 257-0031, Japan; and § Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan
AuthorAffiliation_xml – name: RIKEN BioResource Center, RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan; † Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan; ‡ BioScience Research Laboratory, Fujiya Co., Ltd., Hadano 257-0031, Japan; and § Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan
Author_xml – sequence: 1
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  surname: Fukami-Kobayashi
  fullname: Fukami-Kobayashi, Kaoru
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  fullname: Shiina, Takashi
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Edited by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, and approved May 17, 2005
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: MIC, MHC class I chain-related molecule; LINE, long interspersed nuclear element; Myr, million years; GFD, genome fragments duplication; SINE, short interspersed nuclear element.
Author contributions: H.I. and Y.T. designed research; T.S., T.A., K.S., M.Y., and H.I. performed research; K.F.-K. and Y.T. analyzed data; and Y.T. wrote the paper.
To whom correspondence should be addressed. E-mail:ytateno@genes.nig.ac.jp.
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Snippet 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...
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StartPage 9230
SubjectTerms Animals
Apes
Biological Sciences
Chimpanzees
Divergent evolution
Evolution
Evolution, Molecular
Genes, MHC Class I - genetics
Genome
Genomes
Genomics
Histocompatibility Antigens Class I - genetics
HLA-B Antigens - genetics
HLA-C Antigens - genetics
Humans
Long Interspersed Nucleotide Elements
Macaca mulatta
Mica
Molecules
Monkeys
Pan troglodytes
Primates
Protein Structure, Tertiary
Regional identity
Time Factors
Title Genomic Evolution of MHC Class I Region in Primates
URI https://www.jstor.org/stable/3375878
http://www.pnas.org/content/102/26/9230.abstract
https://www.ncbi.nlm.nih.gov/pubmed/15967992
https://www.proquest.com/docview/201301652
https://www.proquest.com/docview/17634550
https://www.proquest.com/docview/67990916
https://pubmed.ncbi.nlm.nih.gov/PMC1153716
http://doi.org/10.1073/pnas.0500770102
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