Setting timescales for epigenetic switching
Quantitative gene regulation at the population level can be achieved by two fundamentally different modes of regulation at individual gene copies. A “digital” mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an “analog” mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), “digital” Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modelling, we find that FLC expression before cold is regulated by both analog and digital modes. We demonstrate a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, allowing subsequent digital silencing, where these copies switch OFF stochastically and heritably without cold. The timescale of this one-way switch is governed by the strength of transcription: high transcription prevents switching, while low levels of transcription allow for rapid switching. In this way, analog and digital regulation are combined: analog regulation precedes digital with a time delay for the switch depending on the strength of transcription. Overall, our data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.