Frazer_Supp. Fig. Legends
Supplemental Figure 1 Isolation of DNA sequences orthologous to the human 21q SIM2 interval in multiple mammalian species. a, A 280 kb region on human 21q containing SIM2 and part of the holocarboxylase synthetase (HLCS) genes was targeted for multi-species sequence comparison. The position of this 280 kb interval on the NCBI sequence contig NT_002836 (http://www.ncbi.nlm.nih.gov/) is shown. A total of 14 universal overgo probes were designed based on human-mouse sequence conservation (Supplemental Table 1) and used to screen genomic DNA BAC clone libraries of the horse, cow, pig, cat, and mouse. b, A horse BAC contig map was constructed by STS-content mapping and restriction enzyme digest-based DNA fingerprinting of 24 clones isolated from the horse BAC library. A minimally overlapping set of BAC clones (shown in blue) was chosen from this complete BAC contig map. c, The minimally overlapping set of BACs selected from the horse, cow, pig, dog, cat, and mouse complete BAC contig maps for hybridization to the human 21q arrays are shown.
Supplemental Figure 2 Visualization plots showing the locations of conserved human chromosome 21 sequences in the 365 kb interval surrounding SIM2. In each of the 40 individual plots a 10 kb region on human 21q is depicted (to view all the plots use the scroll bar to move down). The top panel in each plot indicates the human 21q position ranging from base pair 23520000 to 23885000 on NCBI sequence contig NT_002836. The names of the genes (SIM2 and HLCS), the locations of their exons (color-coded rectangles) and the direction of transcription are indicated in the second panel (see plots on pages 15-40). In the panel labeled, “Horse conserved regions”, the locations of human-horse conserved elements (≥ 30 bp and 60% conformance) identified by hybridizing 21q arrays with horse BAC DNA are indicated by purple rectangles. The panel labeled, “Horse array”, consists of a curve that represents the level of sequence conservation between humans and horses graphed on a vertical scale (0-100% conformance) relative to the coordinates in the human sequence. Peaks representing conserved human-horse elements rise above the veil, which is set at 60% conformance, and are highlighted purple. Human conserved sequences identified by hybridizing the 21q arrays with cow, pig, dog, cat, and mouse BAC DNA are shown as color-coded rectangles and curves in the following 5 sets of panels. Peaks that rise above the veil but are not color-coded represent sequences that have ³ 60% conformance but are low complexity (see Supplemental algorithm description). The panel labeled, “repeat”, shows the positions of interspersed repeats, which were not tiled on the 21q arrays, and thus, the corresponding conformance information is absent. In the second to last panel labeled, “Mouse alignment conserved regions”, the locations of human-mouse conserved elements (≥ 100 bp and 80% conformance) identified by analyzing BLASTZ alignment data with a sliding window are indicated by rectangles. The panel labeled, “Mouse alignment”, consists of a curve that represents the level of sequence conservation between humans and mice graphed on a vertical scale (50-100% identity) relative to the coordinates in the human sequence. Peaks representing conserved human-mouse sequences in the BLASTZ alignment data rise above the veil, which is set at 80% identity, and are highlighted blue.