Loops matter

Michlewski et al (2008) show that many miRNA loop regions have been well conserved during vertebrate evolution, and have unanticipated roles in miRNA processing and regulation.

Promoter evolution across mammals

Taylor et al (2006) perform the largest study to date of evolutionary rates in mammalian promoters, allowing detailed comparisons between different promoter classes for the first time. This is also the first demonstration of the unusually accelerated sequence evolution within primate promoters.

An atlas of mammalian promoter anatomy

Carninci et al (2005): one of the first large CAGE sequencing studies, discovering several hundred thousand transcription start sites (TSSs) in the mouse and human genomes. The datasets allowed quantitative analysis of promoter usage in different tissues and showed that differentially regulated alternative TSSs for the same gene are common across the genome.