Recently, in collaboration with the Lynch Lab, I employed CAGE to identify active promoters in the microcrustacean Daphnia pulex. This was the first comprehensive study of cis-regulatory regions in any crustacean and provided insight into the regulation of gene expression in D. pulex, an emerging model organism.
I’m also keenly interested in the population genetics of cis-regulatory regions, and fortunately Daphnia is an excellent system in which to explore this. Future work will concern variation and selection at cis-regulatory regions in six well-defined natural populations of D. pulex.
Our investigations involve large amounts of computation and tailored analysis workflows, so I also develop software related to promoter identification. An R/Bioconductor package I wrote, ‘TSRchitect’, is currently in the latter stages of testing and will be released to the community later this year.