An inferred model of the Bacillus subtilis global transcriptional regulatory network
Event details
| Date | 16.06.2014 |
| Hour | 14:00 |
| Speaker | Prof. Patrick Eichenberger, Department of Biology, New York University |
| Location | |
| Category | Conferences - Seminars |
We present a global model of the Bacillus subtilis gene regulation network. Our model is based on the analysis of two large transcriptomics datasets (a public dataset from the BaSysBio consortium and our more recently collected dataset that includes many time series over a variety of experimental conditio ns). In order to identify potentially causative relationships between transcription regulators (such as DNA binding proteins and small regulatory RNAs) and their target genes, we used an updated version of the network inference algorithm Inferelator . Our novel computational approach integrates previously validated network edges (priors) and estimated transcription factor activities (TFA) to dramatically improve the accuracy of the predictions. Our model currently incorporates 240 putative regulators and pre dicts 4,348 regulatory interactions. About a quarter of these interactions are dependent on alternative sigma factors. We show that a majority of these predictions are supported in microarray experiments comparing wild type to mutant strains (where the gen e encoding the regulator of interest has been knocked out). Our network model will help to accelerate the pace of gene function discovery in B. subtilis and other Gram - positive species. Initial exploration of the model reveals many genes of previously unkn own function that are co - regulated with other genes involved in various aspects of B. subtilis biology, including sporulation, biofilm formation, competence, motility, stress responses and metabolism. As an example of functional validation of the network p redictions, we highlight the characterization of a novel group of sporulation genes encoding enzymes involved in spore polysaccharide synthesis.
Bio: After studying Biochemistry and Molecular Biology, I obtained my Ph.D. from the University of Geneva in 1997. My doctoral work in the laboratory of Prof. Hans Geiselmann focused on the analysis of mechanisms of transcriptional activation in the bacterium Escherichia coli. Then, as a post-doctoral fellow, I moved to the laboratory of Prof. Richard Losick at Harvard, where I spent six wonderful years investigating various aspects of sporulation in Bacillus subtilis with a special emphasis on genome-wide identification of sporulation genes. I joined NYU Biology’s department as an Assistant Professor in October 2004.
Bio: After studying Biochemistry and Molecular Biology, I obtained my Ph.D. from the University of Geneva in 1997. My doctoral work in the laboratory of Prof. Hans Geiselmann focused on the analysis of mechanisms of transcriptional activation in the bacterium Escherichia coli. Then, as a post-doctoral fellow, I moved to the laboratory of Prof. Richard Losick at Harvard, where I spent six wonderful years investigating various aspects of sporulation in Bacillus subtilis with a special emphasis on genome-wide identification of sporulation genes. I joined NYU Biology’s department as an Assistant Professor in October 2004.
Practical information
- Informed public
- Free
Organizer
- UPKIN, Laboratory of Microbiology and Microsystems