Integrating analog and digital modes of gene expression at <i>Arabidopsis FLC</i>.

Abstract

Quantitative gene regulation at the cell 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 <i>Arabidopsis</i> floral repressor <i>FLOWERING LOCUS C (FLC),</i> 'digital' Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether <i>FLC</i> regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of <i>FLC</i> mRNA and protein, together with mathematical modeling, we find that <i>FLC</i> expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual <i>FLC</i> gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in <i>FLC</i> expression at the cell population level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.