ABSTRACT
This chapter shows how Cap Analysis of Gene Expression (CAGE) can be combined with other genomic resources, in particular cross-species alignments and polymorphism data investigating the general trends in mammalian promoter evolution. It illustrates the considerable advantages, and the limitations, of CAGE data for the definition of transcription start sites (TSS) and promoter regions. The chapter highlights insights into gene regulation and evolutionary processes that have come largely from CAGE based evolutionary analysis. It demonstrates how high quality and precise TSS definitions can be used to investigate the spatial distribution of constraints in TSS flanking regions and differences in the pattern of constraint between promoter categories. Comparative genomics together with CAGE derived promoter regions have allowed important insights into the complex evolutionary dynamics of promoters across mammalian orders. The expanding empirical data on transcription factor binding sites within promoters may offer important insights into the evolutionary behaviour of functional sites.
