A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting
Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours;
however, state-of-the-art measurements have revealed that many of the molecular …
however, state-of-the-art measurements have revealed that many of the molecular …
[HTML][HTML] Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage
The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and
cleavage of the nascent RNA transcript. Although each of these steps can be regulated as …
cleavage of the nascent RNA transcript. Although each of these steps can be regulated as …
Stochastic modeling of the mRNA life process: A generalized master equation
C Shi, X Yang, J Zhang, T Zhou - Biophysical Journal, 2023 - cell.com
The mRNA life cycle is a complex biochemical process, involving transcription initiation,
elongation, termination, splicing, and degradation. Each of these molecular events is …
elongation, termination, splicing, and degradation. Each of these molecular events is …
[HTML][HTML] Regulation of the dynamic RNA Pol II elongation rate in Drosophila embryos
An increasing number of studies have shown the key role that RNA polymerase II (RNA Pol
II) elongation plays in gene regulation. We systematically examine how various enhancers …
II) elongation plays in gene regulation. We systematically examine how various enhancers …
[HTML][HTML] Statistics of nascent and mature RNA fluctuations in a stochastic model of transcriptional initiation, elongation, pausing, and termination
T Filatova, N Popovic, R Grima - Bulletin of Mathematical Biology, 2021 - Springer
Recent advances in fluorescence microscopy have made it possible to measure the
fluctuations of nascent (actively transcribed) RNA. These closely reflect transcription kinetics …
fluctuations of nascent (actively transcribed) RNA. These closely reflect transcription kinetics …
Deciphering a global source of non-genetic heterogeneity in cancer cells
J Zhang, X Han, L Ma, S Xu, Y Lin - Nucleic Acids Research, 2023 - academic.oup.com
Cell-to-cell variability within a clonal population, also known as non-genetic heterogeneity,
has created significant challenges for intervening with diseases such as cancer. While non …
has created significant challenges for intervening with diseases such as cancer. While non …
Mean-field theory accurately captures the variation of copy number distributions across the mRNA life cycle
J Szavits-Nossan, R Grima - Physical Review E, 2022 - APS
We consider a stochastic model where a gene switches between two states, an mRNA
transcript is released in the active state, and subsequently it undergoes an arbitrary number …
transcript is released in the active state, and subsequently it undergoes an arbitrary number …
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from
promoter-proximal pausing are key rate-limiting steps in gene expression. These processes …
promoter-proximal pausing are key rate-limiting steps in gene expression. These processes …
Decoding the grammar of transcriptional regulation from RNA polymerase measurements: models and their applications
The genomic revolution has indubitably brought about a paradigm shift in the field of
molecular biology, wherein we can sequence, write and re-write genomes. In spite of …
molecular biology, wherein we can sequence, write and re-write genomes. In spite of …
The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian
Gene expression inherently gives rise to stochastic variation (“noise”) in the production of
gene products. Minimizing noise is crucial for ensuring reliable cellular functions. However …
gene products. Minimizing noise is crucial for ensuring reliable cellular functions. However …