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Gene expression in growing cells: A biophysical primer
Paper Information
Authors: Ido Golding (University of Illinois at Urbana-Champaign), Ariel Amir (Harvard University, Weizmann Institute)
Journal: Reviews of Modern Physics, Vol. 96, October–December 2024
Published: 4 October 2024
Colloquium-Gene expression in growing cells-A biophysical primer.pdf
Abstract Summary
This review surveys the emerging paradigm of cell-cycle coupled gene expression, with emphasis on global expression patterns rather than gene-specific regulation. The paper addresses fundamental questions:
- How do mRNA and protein levels scale with cell volume and cell-cycle progression?
- What are the molecular origins of observed scaling laws?
- What are the consequences of cell-cycle dependence for heterogeneity (“noise”) in gene expression?
The paper discusses both growth-agnostic(불가지론) models (constant-rate models) and growth-dependent models that account for DNA replication, transcription/translation constraints, and cell-cycle effects.
Key Concepts
Main Themes
- Growth-agnostic models: Traditional constant-rate gene expression models that ignore cell cycle
- Growth-dependent models: Models incorporating DNA replication, RNAP/ribosome availability
- Cell-cycle coupling: How periodic cellular processes modulate gene expression
- Stochasticity: Inherent randomness in synthesis, degradation, and cell division partitioning
- Resource limitation: Competition for limited RNA polymerase and ribosomes
Three Regimes of Continuous Growth Model
- Regime I: RNAP-limited transcription, ribosome-limited translation
- Regime II: DNA-limited transcription, ribosome-limited translation
- Regime III: DNA-limited transcription, mRNA-limited translation