Comparative genomics of cis-regulatory elements in Cytokinin Response Factors across the plant taxa

Abstract

Expression patterns of genes are controlled by short regions of DNA in promoter regions known as cis-regulatory elements. How expression patterns change due to alterations in cis-regulatory elements after genes duplicate are not well studied in plants. Over 300 promoter sequences from a small, well-conserved family of plant transcription factors known as Cytokinin Response Factors (CRFs) were examined for conserved motifs throughout the evolutionarily diverged clades seen in Angiosperms. Both general CRF plant family as well as distinct clade specific motifs were found. Once identified, significantly enriched motifs were then compared to known transcription factor binding sites to elucidate potential functional roles. Additionally, presence of similar motifs shows that levels of conservation exist between different CRFs across the kingdom plantae likely occurring through processes of neo- or sub-functionalization. Furthermore, significant patterns of motif conservation are seen within and between CRF clades suggesting cis-regulatory regions have been conserved through CRF evolution.