Integrating analog and digital modes of gene expression at Arabidopsis FLC

Quantitative gene regulation can be achieved in two ways: “digital” or “analog”. “Digital” refers to binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state. “Analog” refers to graded expression levels at each gene copy. In response to cold, the Arabidopsis floral repressor FLOWERING LOCUS C (FLC) exhibits digital Polycomb silencing, facilitating quantitative epigenetic memory. However, whether analog or digital regulation is involved before cold is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modelling, we find both analog and digital modes of FLC regulation and demonstrate temporal separation between the two, with analog preceding digital. Intermediate analog FLC expression levels subsequently allow slow population-level digital silencing, where individual gene copies switch OFF stochastically and heritably without cold. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways are integrated.