Colloquia Archive
Constructing Models of Gene Regulatory Networks for Cell Fate Specification
April 18, 2008
Co-sponsored by the Center for Computational Biology and Bioinformatics.Host: Yaoqi Zhou
AbstractTranscription factors regulate the expression of genes by binding to specific sites on the DNA that are typically spatially close to sequences that code for proteins. A group of such binding sites is collectively known as a cis-regulatory region. Once at their sites, the regulators act by influencing the rates of transcription of the gene. When a gene processes the effects of multiple transcription factors, one can view it as performing a computation. The inputs are the occupancies of the binding sites in the cis-regulatory region and the output is the rate of transcription. Using a simple chemical kinetic model, I will show how a particular gene regulatory network controls the differentiation of cells in the immune system. Then, I will present an approach for inferring information about synergies between transcription factors acting at each node in the network from single-cell data. The latter analysis, which is based on a stochastic treatment of gene expression, enables elucidation of combinatorial effects in gene regulatory networks without fitting.
BiographyAaron Dinner is an assistant professor in the Chemistry Department at the University of Chicago. He received his A.B. from Harvard University in 1994 and his Ph.D. in 1999. Prof. Dinner won a Dreyfus New Faculty Award in 2003 and an NSF Career Award in 2006. He is also a Searle Scholar. The Dinner group develops and applies theoretical methods for relating cellular behavior to molecular properties. They are particularly interested in how proteins regulate access to genes in the context of the development of the immune system, which has direct implications for treating autoimmune pathologies and improving gene therapy and vaccination strategies.
