An important question when studying gene regulation is which transcription factors (TFs) interact with which cis-regulatory elements, such as promoters and enhancers. Addressing this issue in complex multicellular organisms is challenging as several hundreds of TFs and thousands of regulatory elements must be considered in the context of different tissues and physiological conditions. Yeast one-hybrid (Y1H) assays provide a powerful “gene-centered” method to identify the TFs that can bind a DNA sequence of interest. In this introduction, we describe the basic principles of the Y1H assay and its advantages and disadvantages and briefly discuss how it is complementary to “TF-centered” methods that identify protein-DNA interactions for a known protein of interest.
Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. (2016). Gene-Centered Yeast One-Hybrid Assays. Cold Spring Harb. Prot., 2016(12).
TF–cofactor protein–protein interaction network from Reece‐Hoyes et al (2013) was used to predict activators and repressors. Blue, predicted repressors; red, predicted activators; yellow, cofactors; blue outline, co‐repressors; red outline, co‐activators.
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein–DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene‐centered metazoan PDI network to date by examining interactions between 90% of C. elegans TFs and 15% of gene promoters. We used this network as a backbone to predict TF binding sites for 77 TFs, two‐thirds of which are novel, as well as integrate gene expression, protein–protein interaction, and phenotypic data to predict regulatory and biological functions for multiple genes and TFs.
Fuxman Bass, JI, Pons, C, Kozlowski, L, Reece‐Hoyes, JS, Shrestha, S, Holdorf, AD, Mori, A, Myers, CL, Walhout, AJM. (2016). A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions. Mol. Sys. Biol. 12: 884. doi: 10.15252/msb.20167131
Best wishes to Dr. Juan Fuxman Bass who has left the lab to start his own lab as an Assistant Professor in the Department of Biology at Boston University. He will be working on transcription factors that regulate the immune response. We will miss you Juan!
The Walhout lab participated in the annual joint Cancer Center for Systems Biology (CCSB) and Program in Systems Biology (PSB) retreat in Gloucester, MA, on September 7-9. The retreat attendees heard talks from their colleagues in CCSB and PSB, as well as lectures form other invited speakers. Distinguished Professor John Roth of UC Davis opened the retreat with a historical perspective of his work on mutation selection in bacteria. University of Toronto Professor and Howard Hughes Medical Institute Senior International Research Scholar Charlie Boone presented the keynote lecture on genetic networks in yeast, and Tufts University Professor and Howard Hughes Medical Institute Professor David Walt discussed how basic science research lead to the co-founding of the company Illumina. Walhout lab post-doctoral fellows Jingyan Zhang and Huimin Na, and graduate student Aurian Garcia-Gonzalez all gave short talks about their exciting research on C. elegans networks.
Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with metabolic plasticity and thus a selective advantage on different diets in the wild.
Watson E, Olin-Sandoval V, Hoy MJ, Li C, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJM (2016) Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. eLife, doi: 10.7554/eLife.17670
University of Massachusetts Medical School Chancellor Michael Collins presenting the Chancellor’s Award for Outstanding Research to Dr. Emma Watson
Citing the profound, insightful, scientific and, in some cases, jovial words of others, Graduate School of Biomedical Sciences Dean Anthony Carruthers, PhD, reminded the crowd assembled in the Albert Sherman Center Cube on Thursday, June 2, to occasionally revisit the fertile grounds of the scientific giants who preceded them.
“Their legacy is the scientific foundation that shapes all we do,” said Dean Carruthers, professor of biochemistry and molecular pharmacology, during the GSBS Celebration of Student Achievement.
Emma Watson Diet-Responsive Gene Networks Rewire Metabolism in the Nematode Caenorhabditis elegans to Provide Robustness Against Vitamin B12 Deficiency
Marian Walhout, PhD, mentor
Dr. Watson is currently a post-doctoral fellow in Stephen Elledge’s lab at Harvard Medical School.