Development is typically studied in laboratory conditions that have been optimized for growth, and the environmental influence on gene expression is often overlooked. We have performed extensive characterizations of gene expression during L1 arrest and growth by measuring mRNA levels and RNA Polymerase II location genome-wide. These studies show that nutrient availability has a profound influence on gene expression while comprehensively defining the transcriptional response to starvation in this developmental system.

A transcriptional regulatory network for the starvation response

We seek to understand how environmental and developmental control of gene expression are integrated mechanistically. Different cell types have different energy demands and developmental constraints, and we are currently extending our expression analysis to resolve tissue-specific starvation responses. With conditional, temporal and anatomical control of expression defined, we will use bioinformatics to infer cis-regulatory sequences that mediate tissue-specific nutritional control of expression. C. elegans is amenable to high-throughput DNA transformation and we are well positioned to test predicted regulatory sequences in vivo and to dissect their function with mutational analysis. With bona fide regulatory elements in hand, we will identify the transcription factors and signaling pathways that regulate them working toward a gene regulatory network model for the starvation response.