TY - JOUR
T1 - Gene expression in growing cells: A biophysical primer
AU - Golding, Ido
AU - Amir, Ariel
N1 - We are grateful to Tianyou Yao for preparing the manuscript figures. We thank Andrew Pountain, Seunghyeon Kim, Sangjin Kim and Itai Yanai for sharing unpublished results. We are grateful to Sven van Teeffelen, Jie Lin and Teemu Miettinen for valuable comments. Work in the Golding lab is supported by the National Institutes of Health grant R35 GM140709 and by the Alfred P. Sloan Foundation. AA was supported by NSF CAREER 1752024 and by the Clore Center for Biological Physics.
PY - 2023/11/20
Y1 - 2023/11/20
N2 - Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until recently, there was little dialog between the two areas of study. Most theoretical models for gene regulation assumed gene activity to be oblivious to the progression of the cell cycle between birth and division. But there are numerous ways in which the periodic character of all cellular observables can modulate gene expression. The molecular factors required for transcription and translation increase in number during the cell cycle, but are also diluted due to the continuous increase in cell volume. The replication of the genome changes the dosage of those same cellular players but also provides competing targets for regulatory binding. Finally, cell division reduces their number again, and so forth. Stochasticity is inherent to all these biological processes, manifested in fluctuations in the synthesis and degradation of new cellular components as well as the random partitioning of molecules at each cell division. The notion of gene expression as stationary is thus hard to justify. In this review, we survey the emerging paradigm of cell-cycle regulated gene expression, with an emphasis on the global expression patterns rather than gene-specific regulation. We discuss recent experimental reports where cell growth and gene expression were simultaneously measured in individual cells, providing first glimpses into the coupling between the two. While the experimental findings, not surprisingly, differ among genes and organisms, several theoretical models have emerged that attempt to reconcile these differences and form a unifying framework for understanding gene expression in growing cells.
AB - Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until recently, there was little dialog between the two areas of study. Most theoretical models for gene regulation assumed gene activity to be oblivious to the progression of the cell cycle between birth and division. But there are numerous ways in which the periodic character of all cellular observables can modulate gene expression. The molecular factors required for transcription and translation increase in number during the cell cycle, but are also diluted due to the continuous increase in cell volume. The replication of the genome changes the dosage of those same cellular players but also provides competing targets for regulatory binding. Finally, cell division reduces their number again, and so forth. Stochasticity is inherent to all these biological processes, manifested in fluctuations in the synthesis and degradation of new cellular components as well as the random partitioning of molecules at each cell division. The notion of gene expression as stationary is thus hard to justify. In this review, we survey the emerging paradigm of cell-cycle regulated gene expression, with an emphasis on the global expression patterns rather than gene-specific regulation. We discuss recent experimental reports where cell growth and gene expression were simultaneously measured in individual cells, providing first glimpses into the coupling between the two. While the experimental findings, not surprisingly, differ among genes and organisms, several theoretical models have emerged that attempt to reconcile these differences and form a unifying framework for understanding gene expression in growing cells.
U2 - https://doi.org/10.48550/arXiv.2311.12143
DO - https://doi.org/10.48550/arXiv.2311.12143
M3 - مقالة
SN - 2331-8422
JO - arxiv.org
JF - arxiv.org
ER -