Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions of the genome. As current GRN mapping methods test one TF at a time and require the use of cells harboring the mutation(s) of interest, they are not suitable to identify TFs that bind to wild-type and mutant loci. Here, we use gene-centered yeast one-hybrid (eY1H) assays to interrogate binding of 1,086 human TFs to 246 enhancers, as well as to 109 non-coding disease mutations. We detect both loss and gain of TF interactions with mutant loci that are concordant with target gene expression changes. This work establishes eY1H assays as a powerful addition to the toolkit of mapping human GRNs and for the high-throughput characterization of genomic variants that are rapidly being identified by genome-wide association studies.
Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJM. (2015) Human Gene-Centered Transcription Factor Networks for Enhancers and Disease Variants. Cell 161:661–73. Cell
Dr. Lesley MacNeil has left the lab to start her own lab as an Assistant Professor in the Department of Biochemistry and Biomedical Sciences at the Farncombe Family Digestive Health Research Institute at McMaster University in Hamilton, Ontario, Canada. We will miss her, but we are very excited for her. Go Les, Go Canada!
RNAi has become an essential tool in C. elegans research. This unit describes procedures for RNAi in C. elegans by microinjecting with dsRNA, feeding with bacteria expressing dsRNA, and soaking in dsRNA solution, as well as high-throughput methods for RNAi-based screens.
Micronutrients are required in small proportions in a diet to carry out key metabolic roles for biomass and energy production. Humans receive micronutrients either directly from their diet or from gut microbiota that metabolize other nutrients. The nematode Caenorhabditis elegans and its bacterial diet provide a relatively simple and genetically tractable model to study both direct and microbe-mediated effects of micronutrients. Recently, this model has been used to gain insight into the relationship between micronutrients, physiology, and metabolism. In particular, two B-type vitamins, vitamin B12 and folate, have been studied in detail. Here we review how C. elegans and its bacterial diet provide a powerful interspecies systems biology model that facilitates the precise delineation of micronutrient effects and the mechanisms involved.
Yilmaz, LS and Walhout AJ. (2014) Worms, bacteria, and micronutrients: an elegant model of our diet. Trends Genetics. 30, 496-503. PubMed, Trends Genetics
Diet greatly impacts metabolism in health and disease. In response to the presence or absence of specific nutrients, metabolic gene regulatory networks sense the metabolic state of the cell and regulate metabolic flux accordingly, for instance by the transcriptional control of metabolic enzymes. Here, we discuss recent insights regarding metazoan metabolic regulatory networks using the nematode Caenorhabditis elegans as a model, including the modular organization of metabolic gene regulatory networks, the prominent impact of diet on the transcriptome and metabolome, specialized roles of nuclear hormone receptors (NHRs) in responding to dietary conditions, regulation of metabolic genes and metabolic regulators by miRNAs, and feedback between metabolic genes and their regulators.
Watson E and Walhout AJ. (2014) Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy. Trends Endocrinol. Metab. 25, 502-508. PubMed, Trends Endocrinol. Metab.
Walhout lab graduate student Emma Watson received the 2014 Harold M. Weintraub Graduate Student Award for research into the complex interactions between diet, gene expression and physiology. Only 13 students from North America were chosen for the prestigious award sponsored by the Basic Sciences Division of the Fred Hutchinson Cancer Research Center. Fellow UMass graduate student Colin Conine who studies in Craig Mello’s lab also received the Weintraub award.
“I’m happy that both Colin and I won the award this year. I think it’s a testament to the strong community of C. elegans biologists here at UMass Medical School, with whom we have both trained,” said Watson. “We use the roundworm C. elegans to explore basic biological processes and find new angles of attack for human disease. C. elegans was the perfect model for me to study the genetic underpinnings that link diet and physiology. Its metabolic network and nutritional requirements are surprisingly a lot like ours, despite being a soil-dwelling nematode that eats bacteria all day long!”
“Emma is an outstanding graduate student who fully deserves this award,” said Dr. Walhout. “It is a pleasure to work with her. She is hard working, smart, fun and has vision. If she sets the bar, it is very high!”
Watson focuses her research on understanding the effects of diet on the genome, and how this relates to physiology. Using C. elegans and its bacterial diet, Watson developed a novel interspecies model that allows these questions to be addressed systemically. With this new systems biology model, she found that worms fed a diet of vitamin-B12-synthesizing bacteria exhibit altered gene expression and accelerated development compared to worms fed bacteria that cannot synthesize vitamin B12. Watson also found that worms rewire their metabolic network according to B12 availability, especially with regard to propionic acid metabolism, which depends on this essential vitamin and can cause a buildup of toxic metabolites under B12 deficiency.
The Weintraub award, established in 2000, honors the late Harold “Hal” M. Weintraub, PhD, a founding member of Fred Hutchinson’s Basic Sciences Division, who died of brain cancer in 1995 at age 49. Weintraub was an international leader in the field of molecular biology. Among his many contributions, he identified genes responsible for instructing cells to differentiate, or develop, into specific tissues such as muscle or bone. The award honors Weintraub and his enthusiastic support of colleagues, students and young scientists.
Conine and Watson will participate in a scientific symposium on May 2 at Fred Hutchinson Cancer Research Center in Seattle.