The Semple Lab

Myself and Martin Taylor (2009) are invited to write an opinion piece for Science on recent discoveries in chromatin structure and genomic sequence evolution.

Taylor et al (2008) show that claims of widespread positive selection in human promoters are unlikely to explain the elevated substitution rates seen, but a compelling case can be made for mutational bias.

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.

Prendergast et al, 2007: the first genome-wide study of human chromatin structure and evolutionary parameters including mutation and selection, showing a general increase in mutation rates in genomic regions of relatively inaccessible higher order chromatin structure.

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.

A detailed study (Semple et al, 2005) of the evolutionary history of this locus shows evidence for opposing modes of selection over primate history – often at the same sites.

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.