Comparative genomic analysis as a tool for biological discovery

Abstract

The recent completion of the human genome sequence has enabled the identification of a large fraction of our gene catalogue and their physical chromosomal position. However, current efforts lag at defining the cis-regulatory sequences that control the spatial and temporal patterns of each gene's expression. This task remains difficult due to our lack of knowledge of the vocabulary controlling gene regulation and the vast genomic search space, with greater than 95% of our genome being noncoding. Recent comparative genomic-based strategies are beginning to aid in the identification of functional sequences based on their high levels of evolutionary conservation. This has proven successful for comparisons between closely related species such as human-primate or human-mouse, but also holds true for distant evolutionary comparisons, such as human-fish or human-bird. In this review we provide support for the utility of cross-species sequence comparisons by illustrating several applications of this strategy, including the identification of new genes and functional non-coding sequences. We also discuss emerging concepts as this field matures, such as how to properly select which species for comparison, which may differ significantly between independent studies.

Figure 1. Phylogenetic tree of a subset of vertebrate species

The approximate divergence time of each of the eight vertebrate species whose genome sequences are currently available is represented (not drawn to scale). Haploid genome sizes are indicated in million base pairs.

Figure 2. Human versus mouse PDX-1 (IPF1) genomic sequence comparison

VISTA Genome Browser output in which human is the reference sequence with per cent similarity to mouse plotted on the vertical axis (http:/pipeline.lbl.gov). Vertical arrows correspond to highly conserved non-coding sequences that coincide with previously defined gene regulatory elements. Gene orientation (horizontal arrows) and exon location (coloured bars) are provided above each panel.

Figure 3. Phylogenetic shadowing of primate species

A, the alignment and comparison of sequences from multiple species sequences reveal which sequences have been conserved in most species, making them likely candidates for being functionally relevant. B, a sequence variation plot of numerous aligned primate sequences flanking an exon of the LXR-á gene. On the x axis 1200 bp of sequence is depicted, while on the y axis the per cent variation is plotted. Note that the lack of sequence diversity (‘phylogenetic shadow’) corresponds closely with the functional exon interval.