Integrating analog and digital modes of gene expression at Arabidopsis FLC

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 e...

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Published in:eLife 2023-07, Vol.12
Main Authors: Antoniou-Kourounioti, Rea L, Meschichi, Anis, Reeck, Svenja, Berry, Scott, Menon, Govind, Zhao, Yusheng, Fozard, John, Holmes, Terri, Zhao, Lihua, Wang, Huamei, Hartley, Matthew, Dean, Caroline, Rosa, Stefanie, Howard, Martin
Format: Article
Language:English
Subjects:
Arabidopsis
Arabidopsis thaliana
Chromosomes and Gene Expression
Cold
Computational and Systems Biology
Epigenetic inheritance
Epigenetics
FLC
FLC gene
Gene expression
Gene regulation
Gene silencing
Genotype & phenotype
mathematical modeling
Mathematical models
Polycomb group proteins
Proteins
quantitative gene expression
Quorum sensing
RNA
RNA polymerase
Single molecule RNA FISH
Transcription factors
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Summary: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 floral repressor 'digital' Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of mRNA and protein, together with mathematical modeling, we find that 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 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 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.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.79743