Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription

The rate-limiting step of transcriptional activation in eukaryotes, and thus the critical point for gene regulation, is unknown. Combining biochemical analyses of the chromatin transition at the transcriptionally induced PHO5 promoter in yeast with modeling based on a small number of simple assumptions, we demonstrate that random removal and reformation of promoter nucleosomes can account for stochastic and kinetic properties of PHO5 expression. Our analysis suggests that the disassembly of promoter nucleosomes is rate limiting for PHO5 expression, and supports a model for the underlying mechanism of promoter chromatin remodeling, which appears to conserve a single nucleosome on the promoter at all times.