Stochastic Analysis of Chemical Reaction Networks with Applications to Epigenetic Cell Memory
Professor Ruth J. Williams
Department of Mathematics
UC San Diego
ABSTRACT
Epigenetic cell memory, the inheritance of gene expression patterns across subsequent cell divisions, is a critical property of multicellular organisms. Simulation studies have shown how stochastic dynamics and timescale differences between establishment and erasure processes in chromatin modifications (such as histone modifications and DNA methylation) can have a critical effect on epigenetic cell memory.
In this talk, we describe a mathematical framework to rigorously validate and extend beyond these computational findings. Viewing our stochastic model of a chromatin modification circuit as a singularly perturbed, finite state, continuous time Markov chain, we extend beyond existing theory in order to characterize the leading coefficients in the series expansions of stationary distributions and mean first passage times. In particular, we characterize the limiting stationary distribution in terms of a reduced Markov chain, provide an algorithm to determine the orders of the poles of mean first passage times, and describe a comparison theorem which can be used to explore how changing erasure rates affects system behavior. These theoretical tools not only allow us to set a rigorous mathematical basis for the computational findings of prior work, highlighting the effect of chromatin modification dynamics on epigenetic cell memory, but they can also be applied to other singularly perturbed Markov chains especially those associated with chemical reaction networks.
Based on joint work with Simone Bruno, Felipe Campos, Yi Fu and Domitilla Del Vecchio.
