Figure 3

Hypothetical and simplistic models of upstream regulatory information content of spatio-temporally regulated genes of rice. (A) Prototype inducible promoter is comprised of combinations of cis-elements (i.e., colored boxes upstream from the core promoter identified by lowercase letters) that directly interface gene induction/represssion with various environmental and developmental signals. This occurs by virtue of their respective cognate regulatory transcription factors (i.e., TF1, TF2, etc.) that respond to hormonal or other physico-chemical changes in the cell. The spatio-temporal properties of genes are therefore defined by the integration of external and developmental cues through the synergistic interactions of various cis-elements and their cognate regulatory transcription factors. (B) Example of a pattern/trend that could be revealed by phylogenetic footprinting of upstream regulatory sequences of rice genes with potential significance to comparative functional genomics and allele mining. Phylogenetic footprinting has suggested that functional differences between the promoters of genes that vary in spatio-temporal regulation may be due to combinations of divergent regulatory fine-tuner elements (colored squares) and highly conserved core module elements (black squares). Variation in cis-regulatory information content may therefore reveal the genomic basis for variant alleles with unique spatio-temporal properties. This concept may be extrapolated for interspecific comparisons of orthologs and paralogs towards the discovery of potential novel alleles in the genus Oryza. Differences in expression in the absence of apparent upstream sequence variation may be used as basis for targeted analysis of differential methylation (shown with asterisks*) of homologous promoters. This concept may have potential applications for the discovery of epialleles that determine phenotypic variation.