Integrating analog and digital modes of gene expression at Arabidopsis FLC

Author:

Antoniou-Kourounioti Rea L12ORCID,Meschichi Anis3ORCID,Reeck Svenja4ORCID,Berry Scott5ORCID,Menon Govind1ORCID,Zhao Yusheng6ORCID,Fozard John1ORCID,Holmes Terri7ORCID,Zhao Lihua3ORCID,Wang Huamei8,Hartley Matthew9ORCID,Dean Caroline4ORCID,Rosa Stefanie3ORCID,Howard Martin1ORCID

Affiliation:

1. Department of Computational and Systems Biology, John Innes Centre

2. School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow

3. Swedish University of Agricultural Sciences, Plant Biology Department

4. Department of Cell and Developmental Biology, John Innes Centre

5. EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales

6. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

7. Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia

8. College of Life Sciences, Wuhan University

9. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus

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.

Funder

Biotechnology and Biological Sciences Research Council

Vetenskapsrådet

HORIZON EUROPE Marie Sklodowska-Curie Actions

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Reference44 articles.

1. Managing the steady state chromatin landscape by nucleosome dynamics;Ahmad;Annual Review of Biochemistry,2022

2. A Polycomb-based switch underlying quantitative epigenetic memory;Angel;Nature,2011

3. Fca_Alleles_Root_Model;Antoniou-Kourounioti,2023

4. The watershed transform in ITK - discussion and new developments;Beare;The Insight Journal,2006

5. The interaction of PRC2 with RNA or chromatin is mutually antagonistic;Beltran;Genome Research,2016

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