Transcription in living cells: molecular mechanisms of bursting

J Rodriguez, DR Larson - Annual review of biochemistry, 2020 - annualreviews.org
gene regulation at the single-cell level. … or how gene activity or expression is modulated
in response to stimuli, we can obtain a unique and dynamic perspective of gene regulation. …

Single-molecule tracking of transcription protein dynamics in living cells: seeing is believing, but what are we seeing?

T Lionnet, C Wu - Current opinion in genetics & development, 2021 - Elsevier
control mechanisms. Single molecule tracking (SMT) … in the physiological context of the
living cell. Here we review SMT principles, and discuss key TF properties uncovered by live-cell

Predictive biology: modelling, understanding and harnessing microbial complexity

AJ Lopatkin, JJ Collins - Nature Reviews Microbiology, 2020 - nature.com
… value in a wide range of physiological settings. These … metabolism in addition to
transcriptional control to achieve … As enumerated in the above sections, predictive modelling has …

A dynamical paradigm for molecular cell biology

JJ Tyson, B Novak - Trends in cell biology, 2020 - cell.com
… important in understanding some aspect of cell physiology. The model may be relatively simple,
… To connect this abstract mathematical notion to cell physiology we must recognize that a …

Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells

S Berry, M Müller, A Rai, L Pelkmans - Cell Systems, 2022 - cell.com
… concentration is fundamental to cell physiology. While the number of transcripts of a given …
in single cells, including pathways not previously implicated in transcriptional control. However…

Transcription factor dynamics

F Lu, T Lionnet - Cold Spring Harbor Perspectives in …, 2021 - cshperspectives.cshlp.org
… key roles in transcription regulation that are not yet fully understood. The emerging model is
that … Furthermore, in situ studies are necessary to recapitulate physiological chromatin states …

A genetic mammalian proportional–integral feedback control circuit for robust and precise gene regulation

T Frei, CH Chang, M Filo… - Proceedings of the …, 2022 - National Acad Sciences
… universal gene regulatory motif that produces robust perfect adaptation for mammalian cells,
… The importance of homeostasis is clearly exemplified in physiology and medicine, where a …

Transcription factors and DNA play hide and seek

DM Suter - Trends in cell biology, 2020 - cell.com
Gene expression is central to all living systems and subject to a complex regulation all the
way from RNA synthesis to … Transcriptional initiation is the most important point of control in the …

Nonequilibrium thermodynamics in cell biology: Extending equilibrium formalism to cover living systems

X Fang, J Wang - Annual review of biophysics, 2020 - annualreviews.org
… The simplest building blocks of gene circuits are the self-regulators: self-activators and
self-repressors. The corresponding gene regulation processes comprise several kinds of …

Multimodal transcriptional control of pattern formation in embryonic development

NC Lammers, V Galstyan, A Reimer… - Proceedings of the …, 2020 - National Acad Sciences
… The logistic regression is a widely used method of inferring predictive models in processes
control of the transcriptional time window, the model probes the impact of each transcription