Computational DNA motif discovery in plant promoters.

摘要

The regulation of gene expression is driven primarily by transcription factors binding to short DNA sequences. Here three studies related to promoter cis-regulatory motif discovery in plant promoters are presented. In the first study, an exact discriminative seeding DNA motif discovery addressing key issues associated with popular DNA motif discovery algorithms is proposed. The Seeder algorithm outperforms popular motif discovery tools on biological benchmark data. In the second study, the algorithm is applied to the identification of cis-regulatory motifs in seed storage protein gene promoters. Known and new motifs are discovered. In the third study, groups of orthologous genes are identified among five dicotyledonous plant species, and DNA motif discovery is carried out in the proximal promoter sequence within each group. The presence of three large clusters of groups of orthologous promoters sharing similar motifs is revealed.