Use of motif analysis programs to identify putative regulatory elements in the orthologous human promoters of co-regulated bovine genes
Amonida Zadissa1, John McEwan2, Chris Brown
1amonida@sanger.otago.ac.nz, Biochemistry Department, Otago University; 2john.mcewan@agresearch.co.nz, AgResearch
Comparative genomics is essential where the genomic sequence of the agriculturally important ruminants is not available. Mammalian genome sequences, however, have made possible new comparative approaches in the agricultural research field. Since the pattern of gene regulation and the corresponding regulatory controls are often conserved across species, new techniques to identify regulatory elements are now made possible.
In this study, we have investigated 101 bovine mRNAs that are expressed specifically in cardiac muscle. Of these 101 sequences, 63 had a unique match in the human genome. A segment of 1500 bp of the sequence immediately upstream from the transcription start site for each of the mRNAs was retrieved from the human genome. These promoter region sequences were then searched for common motifs using MEME. The results were examined for known regulatory elements by the MatInspector Professional tool and BioPerl programs. This procedure detected putative regulatory elements conserved across human mRNAs and the results are consistent with the bovine expression patterns observed.
Sequencing of the bovine genome has begun and this technique will be applied to identify promoter elements in these sequences as they become available.