Gene Expression in Circadian Rhythms
Circadian rhythms drive daily oscillations of gene expression in tissues throughout the body. We're using next generation sequencing to systematically profile transcriptional rhythms in the nervous system of Drosophila melanogaster. We use a variety of computational tools to perform these analyses, including RNA-seq Unified Aligner (Grant et al. 2011) to align and quantify sequenced reads, and JTK_Cycle (Hughes et al. 2011) to detect rhythmic genes. We've discovered that a considerable number of non-coding RNAs oscillate in the brains of flies (Figure 1). Moreover, we've used this data set to identify uncharacterized transcripts, splicing events, and RNA editing events (e.g. Figure 2).
We are also involved in an initiative to sequence and map the transcriptome of Bicyclus anynana. Bicyclus is an emerging model system for ecology and evolution studies. It is particularly important for investigations of interactions between the environment and morphological or behavioral phenotypes, a phenomenon termed polyphenism. We have collected over 100 gigabases of sequenced RNA and are in the process of assembling and annotating expressed transcripts.