title: Titration and hysteresis in epigenetic chromatin silencing.
abstract: Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of this paper is to examine how the perturbations altering the activity of histone modifying enzymes affect the epigenetic states. We analyze the implications of having the total number of silencing proteins, given by the sum of proteins bound to the nucleosomes and the ones available in the ambient, to be constant. This constraint couples different regions of chromatin through the shared reservoir of ambient silencing proteins. We show that the response of the system to perturbations depends dramatically on the titration effect caused by the above constraint. In particular, for a certain range of overall abundance of silencing proteins, the hysteresis loop changes qualitatively with certain jump replaced by continuous merger of different states. In addition, we find a nonmonotonic dependence of gene expression on the rate of histone deacetylation activity of Sir2. We discuss how these qualitative predictions of our model could be compared with experimental studies of the yeast system under anti-silencing drugs.
authors.affiliation: Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA, USA.
authors.forename: Adel
authors.initials: A
authors.lastname: Dayarian
authors.forename: Anirvan M
authors.initials: AM
authors.lastname: Sengupta
mesh_terms: D000107:Acetylation; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D020868:Gene Silencing; D008957:Models, Genetic; D004718:Saccharomycetales / Q000235:genetics* / Q000378:metabolism; D056565:Sirtuin 2 / Q000235:genetics / Q000378:metabolism; D013269:Stochastic Processes
chemical_list: D002843:Chromatin; D005656:Fungal Proteins; D056565:Sirtuin 2