Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse

Abstract

Del(13)Svea36H (Del36H) is a deletion of approximately 20% of mouse chromosome 13 showing conserved synteny with human chromosome 6p22.1-6p22.3/6p25. The human region is lost in some deletion syndromes and is the site of several disease loci. Heterozygous Del36H mice show numerous phenotypes and may model aspects of human genetic disease. We describe 12.7 Mb of finished, annotated sequence from Del36H. Del36H has a higher gene density than the draft mouse genome, reflecting high local densities of three gene families (vomeronasal receptors, serpins, and prolactins) which are greatly expanded relative to human. Transposable elements are concentrated near these gene families. We therefore suggest that their neighborhoods are gene factories, regions of frequent recombination in which gene duplication is more frequent. The gene families show different proportions of pseudogenes, likely reflecting different strengths of purifying selection and/or gene conversion. They are also associated with relatively low simple sequence concentrations, which vary across the region with a periodicity of approximately 5 Mb. Del36H contains numerous evolutionarily conserved regions (ECRs). Many lie in noncoding regions, are detectable in species as distant as Ciona intestinalis, and therefore are candidate regulatory sequences. This analysis will facilitate functional genomic analysis of Del36H and provides insights into mouse genome evolution.

Figure 1

Pictorial representation of the annotation of the Del36H sequence contig. (Top to bottom) Yellow blocks represent the finished sequence of individual genomic clones forming the tiling path across this region; a black line or block at the start and/or end of a clone represents redundant overlapping sequence. Five tracks show in green the distribution of various types of repeats as defined by RepeatMasker. (Red) The distribution of the fraction of G and C nucleotides, between 0.3 (30%) and 0.7 (70%); (purple) the Relative Simplicity Factor scores; (blue) the cumulative signs plot of RSF scores. Alternating gray and black blocks indicate the segments of interest; odd-numbered segments contain gene clusters and evolutionary breakpoints, even-numbered segments lie between and around these. Arrows show the position of annotated genes, their relative transcriptional orientation, and their type; only genes of type “known” have their gene symbol shown. Dark blue: known genes; light blue: novel CDS genes; orange: novel transcript genes; green: pseudogenes; gray: putative genes.

Figure 2

Location of region on mouse and human chromosomes and dotplot of the breakpoint region. (A) The location of the contig on mouse chromosome 13 and the equivalent regions on human chromosome 6. The segments of interest (0-9) are indicated. Note that on the human chromosome, the regions are split into two blocks, breaking in segment 5. Positions and relative sizes of regions are only approximate; human and mouse chromosomes are shown to different scales. (B) Del36H segment 5 has homology with human chromosome 6p25 and 6p22 at its edges, as well as 3q24 in the center. Between these stretches of homology are two stretches of sequence, BP-1 and BP-2, that do not have any detectable homology with human sequence.

Figure 3

Gene clusters. Panels showing the relative organization of genes in several of the gene clusters present in the region, comparing mouse to human. Human sequences shown at the top, mouse at the bottom, with the relevant chromosomes indicated. Where necessary, human sequence has been reoriented to align with mouse sequence (which is shown in centromere-telomere orientation as in Fig. 1). Figures are not to scale and only show selected genes, not noncluster genes or clusters interspersed within some of these clusters. However, conserved genes and clusters within or immediately neighboring clusters are shown with their current mouse gene symbols below the clusters, with an arrow indicating transcriptional orientation. Phylogenetic trees for three of the clusters (A, B, C) are also shown. (A) The vomeronasal 1 receptor (V1r) cluster. Orange ovals indicate where it could not conclusively be determined whether the pseudogene derived from family h or i. Black dots in the phylogenetic tree mark previously unknown family members. The human sequence has only five V1r genes, all degenerated into pseudogenes, whereas in mouse, the equivalent region houses 67 copies, just over half of which (34) are pseudogenes. An asterisk marks a human pseudogene that is displaced from the V1R cluster and actually located in the histone cluster (asterisk in D). (B) The prolactin cluster. Circled in the phylogenetic tree are the solitary family members in mouse and human, the Gh (growth hormone) gene (yellow) on mouse chromosome 11 and the PRL (prolactin) gene (green) on human chromosome 6. In mouse, the prolactin cluster has greatly expanded (to 26 members, with three pseudogenes), whereas in human, the growth hormone cluster has modestly expanded to an estimated five members. (C) The serpin cluster. In human, only one copy (encircled in the phylogenetic tree) of a member of three subfamilies [SERPINB1 (yellow), SERPINB6 (blue), and SERPINB9 (green)] is present (plus a SERPINB9 pseudogene), whereas in mouse, all three subfamilies have expanded, approximately maintaining the order, although not orientation, of the subfamily members. In mouse, a complete b1-b9-b6 block may have inserted itself in reverse orientation within the b9 cluster after individual genes were locally duplicated and inserted, giving rise to the current configuration. The b9 gene shown with a white oval is a partial gene (only the first two exons, including the first coding exon), and probably qualifies as a pseudogene. The human pseudogene is actually located between the two conserved genes shown at bottom, RIPK1 and NQO2. (D) The histone and butyrophilin clusters. Histone family 1 (Hist1) comprises members of all five histones H1, H2a, H2b, H3, and H4. The clusters are of comparable size in mouse and human, part of the slightly larger size in human mostly accounted for by a higher number of pseudogenes. Genes appear to have been duplicated in several groups of genes, containing successively smaller numbers of genes with conserved relative orientations and order as follows: a group of a single copy of each of the five genes in order and orientation H2b^--H2a⁺-H3⁺-H1^--H4⁺ or its reverse complement (white lollipops), this group minus H1 (yellow), then minus H3 (green), and finally a two-member group also missing H4 (black). A gray background area splitting the histone gene cluster in two contains the butyrophilin (Btn) cluster, represented in human by seven genes and in mouse by only two. The V1r cluster shown in A is actually located immediately left of the Btn cluster, further dividing the two parts of the Hist1 cluster. An olfactory receptor gene cluster is located to the left of the histone gene cluster and an Slc17a cluster within the telomeric end of the telomeric cluster. In both mouse and man, this cluster consists of four genes with conserved orientation. The mouse equivalent of the human TRIM38 gene is positionally conserved, but has the opposite transcriptional orientation. At top, the human HMGN4 gene located between ABT1 and the butyrophilin gene cluster is not present in mouse, and an asterisk shows the position within the centromeric histone gene cluster (i.e., outside of the V1R cluster) of a human V1R pseudogene marked by an asterisk in A.