Gene regulatory and metabolic network structure, function and evolution

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Biological networks describe relationships between biomolecules. We study two types of biological networks and the interactions between them. First, we characterize physical and functional gene regulatory networks that are primary controllers of gene transcription during development and growth, to maintain homeostasis and to respond to environmental cues and insults. We will expand our studies on physical interactions between gene promoters and transcription factors in C. elegans to focus on true functional, tissue-specific regulatory networks in vivo. This will involve the examination of non-transcription factor regulators that affect transcription indirectly. Second, we study metabolic networks that convert nutrients into biomass and energy. We will perform experiments to gain insight into how metabolic networks are wired in different tissues and under different nutritional conditions. In addition, we will continue to develop our WormFlux website to enable data integration and flux balance analysis with selected parameters such as biomass composition and different objective functions. Finally, and importantly, we study how gene regulatory networks affect metabolic networks and vice versa. We will test how intestinal transcription is affected by perturbations in metabolic genes. In addition, we will generate gene expression data under different conditions to examine how gene expression changes influence metabolism. Our data will provide broad phenomenological and deep mechanistic insights, as well as a set of resources for the larger community.