Using Cauliflower to Find Conserved Non-Coding Regions in Arabidopsis

Abstract

A bioinformatics approach is used to analyze the degree of conservation between upstream non-coding regions of cauliflower (Brassica oleracea) and Arabidopsis. The level of homology suggests that comparison of these two species could reveal functional cis-regulatory elements. There is growing interest in comparing genome sequences to identify regulatory regions (Stojanovic et al., 1999). This arises in part from the failure of de novo computational methods to consistently recognize functional promoter elements from single genomes (Loots et al., 2000;Pennacchio and Rubin, 2001). Because genomic regions that have a biological function are often conserved through evolution, non-coding regions conserved between species are more likely to contain regulatory sequences (Stojanovic et al., 1999). Numerous computer programs have been written to extract conserved regions or motifs from orthologous sequences (reviewed elsewhere; Fickett and Wasserman, 2000; Stormo, 2000; Ohler and Niemann, 2001). In addition, several studies have shown that the conserved non-coding sequences (CNS) found using such comparisons often have biological meaning (Hardison, 2000; Kent et al., 2000; Loots et al., 2000) and are enriched in transcription factor binding sites (Levy et al., 2001).