Genomic evolution of MHC class I region in primates

doi:10.1073/pnas.0500770102

Genomic evolution of MHC class I region in primates

^*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

Edited by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, and approved May 17, 2005 (received for review February 9, 2005)

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 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.

Footnotes

↵ ¶ To whom correspondence should be addressed. E-mail: ytateno{at}genes.nig.ac.jp.
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.
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.
↵ ∥ The sequence data used in our analysis are available at the International Nucleotide Sequence Database Collaboration (DDBJ/EMBL/GenBank) under the accession nos. BA000025 (human), BA000041 (chimpanzee), and AB128049 (rhesus monkey).
Freely available online through the PNAS open access option.