Promoter Evolution

CREATED: 200701061305 Author: Ron Shamir

** Identify function modules across species via orthology

• project modules via gene orthology
• SAMBA -> BLAST to find gene orthology <- SAMBA
• conserved function modules are regulated by conserved promoter elements
• evolution of motifs -> transfer of function
• modes of motif evolution ** conservation ** BS evolution ** trans switching ** full switching ** program enrichment ** program abridgement ** switching/buffering
• conclusion: redundancy leads to evolvability

** Characterize substitutions

• Kellis et al 2003, Cliften et al 2003
• form phylogeny of sequence, collect statistics about substitutions
• infer substitution rates among pairs of motifs (all 8-mers in promoter region)
• from graph of motifs with 2 types of edges, high substitution rate and low substitution rate
• plot substitution rate vs normal -> enriched in low sub
• plot conservation rate vs normal -> enriched in high conservation
• clusters => TFBS

** Modeling of evolution and learning

• epistatic intervals