Completing the Walhout lab hat trick of three successfully defended doctoral dissertations in six weeks is Dr. Emma Watson who defended her thesis titled “Diet-responsive gene networks rewire metabolism in the nematode Caenorhabditis elegans to provide robustness against vitamin B12 deficiency.” Dr. Watson is now pursuing post-doctoral training with Dr. Stephen Elledge at Harvard Medical School. Best wishes Emma! Booo-yah!
A wealth of physical interaction data between transcription factors (TFs) and DNA has been generated, but these interactions often do not have apparent regulatory consequences. Therefore, equating physical interaction data with gene regulatory networks (GRNs) is problematic. Here, we comprehensively assay TF activity, rather than binding, to construct a network of gene regulatory interactions in the C. elegans intestine. By manually observing the in vivo tissue-specific knockdown of 921 TFs on a panel of fluorescent transcriptional reporters, we identified a GRN of 411 interactions between 19 promoters and 177 TFs. This GRN shows only a modest overlap with physical interactions, indicating that many regulatory interactions are indirect. We applied nested effects modeling to uncover the information flow between TFs in the intestine that converges on a small set of physical TF-promoter interactions. We found numerous cell non-autonomous regulatory interactions, illustrating tissue-to-tissue communication. Our study illuminates the complexity of gene regulation in the context of a living animal.
MacNeil LT, Pons C, Arda HE, Giese GE, Myers CL, Walhout AJM (2015) Transcription Factor Activity Mapping of a Tissue-Specific In Vivo Gene Regulatory Network. Cell Systems 1, 152-162.
Fifty Shades of Worm is a modern love story to be embraced by all C. elegans scientists. Visionary director Michael Hoy partners with Walhout Films to bring this microscopic romance to life. This trailer premiered during the 2015 International C. elegans Meeting at UCLA.
Gene regulatory networks (GRNs) consist of physical and regulatory interactions between transcription factors (TFs) and their DNA targets. While many disease-associated DNA mutations have been identified in protein coding regions of the human genome, the vast majority of these mutations exist in non-coding regions. This observation suggests that gene regulatory networks are altered in human disease.
Three recently published papers were authored and co-authored by the Walhout lab looking at interaction networks in human disease, and TF specificities in both humans and C. elegans. First, in the April 23 issue of Cell post-doctoral fellow Juan Fuxman Bass and colleagues in the Walhout lab and in the Cancer Center for Systems Biology at the Dana-Farber Cancer Institute, used gene-centered enhanced yeast one-hybrid (eY1H) assays to study binding of 1086 human TFs to 246 enhancers and 109 non-coding disease mutations. They discovered a TF-enhancer interaction network of 2,230 interactions between 246 developmental enhancers and 283 TFs. Using this and other data, they discovered lost and gained interactions in TF coding mutations in human diseases like pituitary hormone deficiency and septo-optic dysplasia. Furthermore, they identified differential TF binding for 109 non-coding mutations of 75 genes associated with a variety of diseases from cancer to immune disorders. For example they identified nine mutations in the enhancer of a gene that causes digit malformation and polydactyly. This data provides a framework for further analysis and mapping of human GNRs, plus demonstrates the utility of eY1H in high-throughput characterization of disease variants.
In a press release form UMMS, Dr. Walhout said, “Up to this point, we’ve only been able to investigate one disease-causing mutation at a time, we now have a robust platform that allows us to interrogate hundreds of mutations in a single experiment. This will help us develop a map of the interactions that make up the networks that control gene expression and determine how mutations in the genome give rise to a variety of human diseases.”
Secondly, the Walhout lab collaborated with Dr. Marc Vidal’s group at Cancer Center for Systems Biology at the Dana-Farber Cancer Institute and Dr. Susan Lindquist’s group at the Whitehead Institute for Biomedical Research to examine several thousand missense mutations in human diseases, which was also published in the April 23 issue of Cell. Using a variety of techniques including quantitative LUMIER assays, yeast two-hybrid (Y2H), and eY1H, they developed an integrated protein-chaperone (PCI), protein-protein (PPI), and protein-DNA interaction (PDI) profile of disease vs non-disease alleles. They discovered that most missense disease mutations appear not to impair protein folding or stability. About 60% of the diseases-associated mutations perturb PPI, while one-half of these mutations caused “edgetic” or specific loss of some, but not all, PPI. For PDI, more than 80% of the TF missense mutations abrogated DNA binding or caused a partial change in PDIs. Taken together, this very large data set establishes an integrated interaction network to help understand genotypes that lead to disease phenotypes, and has implications for developing personalized medical treatments.
Finally, as published online April 23 in eLife, the Walhout lab collaborated with Dr. Timothy Hughes at the Donnelly Center at the University of Toronto to examine C. elegans TF sequence specificities. They used protein binding microarray analysis to categorize and predict the binding specificites of about 40% of the TFs in these animals, and determined potential regulatory roles for previously unknown TFs. These findings can be applied to TF orthologos in humans to better understand TF specificities in human physiology.
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
Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu Y, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási A, Charloteaux B, Hill DE, Hao T, Roth FP, Yu X, Walhout AJM, Lindquist S, Vidal M. (2015) Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders. Cell 161:647–60. Cell
Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR. (2015) Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. eLife. 10.7554/eLife.06967