My work focuses on identification and functional characterization of non-coding RNAs (ncRNAs). In particular how they affect gene expression and function during differentiation. I am also pursuing how the evolution of ncRNAs may have contributed to diversification of metazoan bodyplans.
Genomic tools have provided a better description of the complete transcriptome of diverse metazoans. An unexpected finding has been the huge number of potential ncRNAs. These ncRNAs are implicated in a vast array of processes including regulation of transcription, translation, epigenetic control of chromatin, mono-allelic expression, dosage compensation and silencing. In order to better understand the role of ncRNAs in these processes my lab is focusing on one of the most highly conserved and ncRNA rich regions in metazoan genomes, the Hox complex. The Hox complex is composed of a set of related transcription factors that establish positional identity on the anterior-posterior axis. The Hox complex also contains a diverse suite of ncRNAs including miRNAs, anti-sense transcripts, transcribed enhancers and boundary elements as well as many uncharacterized transcripts. At least two of these ncRNAs, both miRNAs, have homeotic function and attenuate the actions of nearby protein coding Hox genes. The highly orchestrated expression and possibly the conserved organization of this complex may be associated with the function of these ncRNAs.
We have begun to define and visualize these ncRNAs transcripts in fly, beetle, and bee using a combination of tiling microarrays and nascent transcript fluorescent in situ hybridization. In addition, we are using genetics tools to examine the functions of these RNAs with the intent of describing their role in the development of animals. Ultimately, this comparative approach will describe both how these small RNAs function and how their evolution has contributed to the diversification of the animal bodyplan.