The Genom of Homo sapiens.pdf

HUMAN–MOUSE COMPARATIVE GENOMICS 307ABCFigure 3. “Phylogenetic shadowing” of closely related species. (A) The alignment and comparison of sequences from multiple primatespecies reveal sequences that have been conserved across most species, making them candidates for being functionally relevantdue to presumed evolutionary constraint at these sites. (B) Primate-specific phylogenetic shadowing reveals a previously defined exonfor the apolipoprotein B gene (APOB). On the x-axis, a variation score is provided with more negative scores indicating less variableregions, and on the y-axis, 1500 bp of human sequence is displayed. The known APOB exon in this interval is depicted by a solid blackline within the plot. Note the decreased amount of primate variation in regions corresponding to the exon. (C) Primate phylogenetictree based on a single genomic interval. A carefully selected set of species that maximize phylogenetic distance (boxed) can capturethe majority of the phylogenetic shadows and thus can reduce the amount of genomic sequence information required.hind this strategy is to analyze orthologous sequencefrom numerous primate species to increase the sum of theevolutionary distance being compared. Rather than performingonly pair-wise comparisons between human andmouse, phylogenetic shadowing compares a dozen ormore different primate species. The additivity of theseprimate differences robustly defines regions of increasedvariation and “shadows” representing conserved segments(Fig. 3A).In its first use, phylogenetic shadowing proved successfulin the identification of both exons and putativegene regulatory elements (Boffelli et al. 2003). This workgenerated and analyzed 13–17 primate species for severalorthologous genomic segments. Examination of a singleexon from four independent genes revealed highly conservedshadows that overlapped with these functionallyimportant regions (one example is provided in Fig. 3B foran exon of the apolipoprotein B gene). Further analysis ofthe human apolipoprotein (a) gene (apo(a)) revealedhighly conserved motifs embedded within the upstreampromoter region. Functional characterization of thesephylogenetic shadows compared to more variable flankingDNA supported their role in regulating apo(a) expression(Boffelli et al. 2003).