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

Abstract

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 FCERIA 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.

Figure 1

1.7 Mb of a YAC, BAC, and PAC contig between the +P5 and KRTC7 loci. A 1.7-Mb contig constructed by 9 YAC, 8 BAC, and 51 PAC clones is shown with addresses, sizes, markers, and gene contents. BAC and PAC clones subjected to sequencing in Figure 2 are indicated by red letters and lines.

Figure 2

Structural feature of the 1.1-Mb (1,139,684 bp) region from the CD1D gene to the FCER1A gene. (A) An operational contig constructed by an overlapping set of two BAC (456N8 and 527I23; in boxes) and nine PAC clones (810N20, 893N23, 987D5, 713I11, 974O18, 683M11, and 622B6) was subjected to nucleotide sequencing. (B) Gene map. Pink boxes indicate previously mapped genes. Red boxes depict genes newly mapped in this study. Green boxes show possibly expressed sequences. Black boxes refer to pseudogenes. Upper boxes define genes oriented from centromere to telomere (from left to right), whereas lower boxes show the opposite orientation. (C) Location of di-, tri-, tetra-, and penta-nucleotide microsatellite repeats. (D) Plot of the local G + C content in overlapping 200-bp windows. A red line indicates the average G + C content (38.4%). (E) Recognition sites of the restriction enzymes, NotI, BssHII, EagI, and SacI. (F) Plot of the local Alu and LINE repeat contents in overlapping 100-kb windows. Red and blue lines represent Alu and LINE repeats, respectively.

Figure 3

Phylogenetic tree of the olfactory receptor gene family. This phylogenetic tree was constructed employing the neighbor-joining method (Saitou and Nei 1987). Sequences were derived from the conserved region between transmembrane segments 2 and 7 in 156 olfactory receptor genes (five “defective type,”, 11 “expressed gene or gene candidate type” OR genes in 1q21–q22 and 140 human olfactory receptor genes submitted to GenBank). Five major families classified by this phylogenetic tree were designated G1, G2A, G2B, G3A, and G3B according to Rouquier et al. (1998). Blue and yellow boxes indicate the olfactory receptor genes located on 1q21–q22 and 6p21.3, respectively. Purple and orange boxes indicate olfactory receptor genes located on chromosomes 1 and 6, respectively, but within unknown subchromosomal locations.