This workshop will focus on how we can quantitatively measure and catalog in a computable fashion, all protein-protein interactions and other key interactions in various human cell types. Talks from experts will be complemented by extensive discussions.
Co-sponsored by the Icahn School of Medicine at Mount Sinai and the University of Massachusetts Medical School
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.
Congratulations to Dr. Ashlyn Ritter on successfully defending her doctoral dissertation “Complex expression dynamics and robustness in C. elegans insulin networks.” Great job Ash! We are all very proud of you!
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.