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Graded versus ON/OFF control in quantitative gene expression and epigenetic memory.

Caroline Dean1, Martin Howard2

  • 1Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. caroline.dean@jic.ac.uk.

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|March 17, 2026
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Summary

Gene expression is regulated through graded analogue control or ON/OFF digital control. This review explores how transcriptional regulation and epigenetic memory influence these modes, using Arabidopsis FLOWERING LOCUS C (FLC) as a case study.

Keywords:
Epigenetic MemoryMathematical ModellingON/OFF Versus Graded ControlPolycomb SystemQuantitative Gene Expression

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Plant Science

Background:

  • Gene expression levels can be modulated through distinct quantitative control mechanisms.
  • Understanding these regulatory modes is crucial for deciphering gene function and developmental processes.

Purpose of the Study:

  • To review the two primary modalities of gene expression regulation: graded analogue control and ON/OFF digital control.
  • To investigate the transcriptional mechanisms underlying these regulatory modes.
  • To explore the link between epigenetic memory and digital gene expression control.

Main Methods:

  • Literature review and synthesis of existing research on gene expression regulation.
  • Analysis of transcriptional regulation mechanisms.
  • Examination of epigenetic modifications, including histone modifications and DNA methylation.
  • Case study analysis of Arabidopsis FLOWERING LOCUS C (FLC) gene regulation.

Main Results:

  • Two gene expression modalities exist: smooth analogue control and discrete ON/OFF digital control.
  • Digital control is associated with epigenetic memory mediated by trans-factor feedback loops and histone modifications.
  • Graded expression and ON/OFF switching of Arabidopsis FLC are critical for its regulation during development and in response to environmental cues like cold exposure.

Conclusions:

  • Both analogue and digital gene expression modes are established through transcriptional regulation.
  • Epigenetic memory, particularly via histone modifications and feedback loops, is linked to digital control.
  • The Arabidopsis FLC gene exemplifies how both graded and digital expression modes are essential for proper developmental and environmental responses.