Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics
S Luo, Z Wang, Z Zhang, T Zhou… - Nucleic Acids …, 2023 - academic.oup.com
Gene expression in mammalian cells is highly variable and episodic, resulting in a series of
discontinuous bursts of mRNAs. A challenge is to understand how static promoter …
discontinuous bursts of mRNAs. A challenge is to understand how static promoter …
Modeling protein concentrations in cycling cells using stochastic hybrid systems
We analyze a class of time-triggered stochastic hybrid systems where the state-space
evolves as per a linear time-invariant dynamical system. This continuous-time evolution is …
evolves as per a linear time-invariant dynamical system. This continuous-time evolution is …
Enhancement of gene expression noise from transcription factor binding to genomic decoy sites
The genome contains several high-affinity non-functional binding sites for transcription
factors (TFs) creating a hidden and unexplored layer of gene regulation. We investigate the …
factors (TFs) creating a hidden and unexplored layer of gene regulation. We investigate the …
Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes
YT Lin, NE Buchler - Journal of The Royal Society …, 2018 - royalsocietypublishing.org
Single-cell experiments show that gene expression is stochastic and bursty, a feature that
can emerge from slow switching between promoter states with different activities. In addition …
can emerge from slow switching between promoter states with different activities. In addition …
Amplification of noisy gene expression by protein burden: An analytical approach
The overexpression of many proteins can often have a detrimental impact on cellular growth.
This expression-growth coupling leads to positive feedback-any increase of intracellular …
This expression-growth coupling leads to positive feedback-any increase of intracellular …
Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives
Random fluctuations (noise) in gene expression can be studied from two complementary
perspectives: following expression in a single cell over time or comparing expression …
perspectives: following expression in a single cell over time or comparing expression …
Quantifying noise modulation from coupling of stochastic expression to cellular growth: An analytical approach
The overexpression of many proteins can often have a detrimental impact on cellular growth.
This expression-growth coupling leads to positive feedback-any increase of intracellular …
This expression-growth coupling leads to positive feedback-any increase of intracellular …
Information processing in unregulated and autoregulated gene expression
How living cells can reliably process biochemical cues in the presence of molecular noise is
not fully understood. Here we investigate the fidelity of information transfer in the expression …
not fully understood. Here we investigate the fidelity of information transfer in the expression …
High cooperativity in negative feedback can amplify noisy gene expression
Burst-like synthesis of protein is a significant source of cell-to-cell variability in protein levels.
Negative feedback is a common example of a regulatory mechanism by which such …
Negative feedback is a common example of a regulatory mechanism by which such …
Comparative analysis of noise-attenuation mechanisms in gene expression: From single cells to cell populations
Negative feedback regulation is a well-known motif for suppressing deleterious fluctuations
in gene product levels. We systematically compare two scenarios where negative feedback …
in gene product levels. We systematically compare two scenarios where negative feedback …