Comparative genomics of gene regulation—conservation and divergence of cis-regulatory information

We recently witnessed a tremendous increase in genomics studies on gene regulation and in entirely sequenced genomes from closely related species. This has triggered analyses that suggest a wide range of evolutionary dynamics of gene regulation, from rapid turnover of transcription-factor binding sites to conservation of enhancer function across large evolutionary distances. Many examples show that enhancers can evolve beyond recognizable sequence similarity while retaining function. However, bioinformatics approaches are increasingly able to detect conserved regulatory elements through characteristic evolutionary sequence signatures. Cis-regulatory changes are also a major source of morphological evolution, which might be facilitated by many biochemically functional elements that are selectively neutral and by the buffering function of redundant enhancers and ‘shadow’ enhancers.