Integrating analog and digital modes of gene expression at Arabidopsis FLC

Antoniou-Kourounioti, R. L. et al. (2023) Integrating analog and digital modes of gene expression at Arabidopsis FLC. eLife, 12, e79743. (doi: 10.7554/elife.79743) (PMID:37466633) (PMCID:PMC10356135)

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 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 modeling, we find that FLC 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 FLC 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 FLC 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.

• Item Type: Articles
• Keywords: Single molecule RNA FISH, quantitative gene expression, FLC, A. thaliana, mathematical modeling.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Antoniou Kourounioti, Dr Rea Laila
• Authors: Antoniou-Kourounioti, R. L., Meschichi, A., Reeck, S., Berry, S., Menon, G., Zhao, Y., Fozard, J., Holmes, T., Zhao, L., Wang, H., Hartley, M., Dean, C., Rosa, S., and Howard, M.
• College/School: College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
• Journal Name: eLife
• Publisher: eLife Sciences Publications
• ISSN: 2050-084X
• ISSN (Online): 2050-084X
• Published Online: 05 July 2023
• Copyright Holders: Copyright © 2023 AntoniouKourounioti, Meschichi, Reeck et al.
• First Published: First published in eLife 12:e79743
• Publisher Policy: Reproduced under a Creative Commons licence