Addressing the precision-plasticity paradox in metazoan gene regulatory networks

University Of California-San Francisco, San Francisco CA

Investigators

Abstract

This project seeks to discover how intracellular and environmental signals change the repertoire of genes activated by DNA-binding proteins. In a particular cellular, developmental and physiological context, DNA-binding proteins normally operate with precision to control a specific network of target genes. However, changes in cellular or extracellular conditions can increase the plasticity of protein-DNA interactions, such that an entirely different group of genes is targeted. This kind of switch from precision to plasticity may hold the key to proper development in multicellular organism, like humans, and dissecting the underlying mechanisms may improve our understanding of how organisms maintain their well-being in the face of environmental fluctuation. In addition to the expected scientific achievements, tackling this research problem will strengthen and enrich the scientific enterprise by providing training and educational opportunities for two women scientists and for a cohort of undergraduate students, including those who are underrepresented minorities. Classic and state-of-art genetic and molecular approaches used in this project will serve as exciting stimuli for the education of budding scientists, as well as a conceptual framework for reasoning and problem solving for the education of those who choose other career paths. The long-term goal of this research is to understand the molecular mechanisms that generate the remarkable specificity with which gene transcription is regulated in multicellular eukaryotes. Based on prior work in this laboratory, a bipartite model has emerged whereby a given DNA-binding transcriptional regulatory factor (TF) can either operate precisely to regulate a specific set of gene targets or, under conditions that promote plasticity, operate to regulate an entirely different set of genes. The model contends that intra- or extracellular signals create a specific context that governs how the TF will associate with other DNA-binding and non-DNA-binding coregulatory factors to activate distinct networks of gene targets. This model will be tested in the nematode, Caenorhabditis elegans, which offers unique features including a compact genome, facile spatiotemporal analyses in the intact organism, powerful genetics, and a comprehensive suite of genomics tools, including CRISPR/Cas9 genome editing. The research will focus on the precise vs. plastic action of the nuclear hormone receptor TF, NHR-25. Previous results showed that a gradient of NHR-25 activity--set up by differential post-translational sumoylation (SUMO) of the protein--in neighboring cells drives distinct gene networks that result in unique cell fates and subsequent tissue differentiation and organogenesis. The complexity of transcription network control will be addressed experimentally to: define and analyze cell-context dependent NHR-25-SUMO regulatory networks; identify pathways and machineries that enable NHR-25 regulatory plasticity; and prepare materials for enChIP analysis to identify proteins associating at NHR-25 dependent response elements. The results obtained will be broadly relevant to metazoan transcriptional regulation and provide an important foundation for future studies of gene regulation.