Genomic anatomy of a premier major histocompatibility complex paralogous region on chromosome 1q21-q22

Takashi Shiina, Asako Ando, Yumiko Suto, Fumio Kasai, Atsuko Shigenari, Nobusada Takishima, Eri Kikkawa, Kyoko Iwata, Yuko Kuwano, Yuka Kitamura, Yumiko Matsuzawa, Kazumi Sano, Masahiro Nogami, Hisako Kawata, Suyun Li, Yasuhito Fukuzumi, Masaaki Yamazaki, Hiroyuki Tashiro, Gen Tamiya, Atsushi KohdaKatsuzumi Okumura, Toshimichi Ikemura, Eiichi Soeda, Nobuhisa Mizuki, Minoru Kimura, Seiamak Bahram, Hidetoshi Inoko

Research output: Contribution to journalLetterpeer-review

29 Citations (Scopus)


Human chromosomes 1q21-q25, 6p21.3-22.2, 9q33-q34, and 19p13.1-p13.4 carry clusters of paralogous loci, to date best defined by the flagship 6p MHC region. They have presumably been created by two rounds of large-scale genomic duplications around the time of vertebrate emergence. Phylogenetically, the 1q21-25 region seems most closely related to the 6p21.3 MHC region, as it is only the MHC paralogous region that includes bona fide MHC class I genes, the CD1 and MR1 loci. Here, to clarify the genomic structure of this model MHC paralogous region as well as to gain insight into the evolutionary dynamics of the entire quadriplication process, a detailed analysis of a critical 1.7 megabase (Mb) region was performed. To this end, a composite, deep, YAC, BAC, and PAC contig encompassing all five CD1 genes and linking the centromeric +P5 locus to the telomeric KRTC7 locus was constructed. Within this contig a 1.1-Mb BAC and PAC core segment joining CD1D to FCER1A was fully sequenced and thoroughly analyzed. This led to the mapping of a total of 41 genes (12 expressed genes, 12 possibly expressed genes, and 17 pseudogenes), among which 31 were novel. The latter include 20 olfactory receptor (OR) genes, 9 of which are potentially expressed. Importantly, CD1, SPTA1, OR, and FCER1A belong to multigene families, which have paralogues in the other three regions. Furthermore, it is noteworthy that 12 of the 13 expressed genes in the 1q21-q22 region around the CD1 loci are immunologically relevant. In addition to CD1A-E, these include SPTA1, MNDA, IFI-16, AIM2, BL1A, FY and FCERIA. This functional convergence of structurally unrelated genes is reminiscent of the 6p MHC region, and perhaps represents the emergence of yet another antigen presentation gene cluster, in this case dedicated to lipid/glycolipid antigens rather than antigen-derived peptides.

Original languageEnglish
Pages (from-to)789-802
Number of pages14
JournalGenome Research
Issue number5
Publication statusPublished - 2001 May


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