Modeling bursty transcription and splicing with the chemical master equation

G Gorin, L Pachter - Biophysical Journal, 2022 - cell.com
Splicing cascades that alter gene products posttranscriptionally also affect expression
dynamics. We study a class of processes and associated distributions that emerge from …

Alternative-splicing-mediated gene expression

Q Wang, T Zhou - Physical Review E, 2014 - APS
Alternative splicing (AS) is a fundamental process during gene expression and has been
found to be ubiquitous in eukaryotes. However, how AS impacts gene expression levels …

Connecting protein and mRNA burst distributions for stochastic models of gene expression

V Elgart, T Jia, AT Fenley, R Kulkarni - Physical biology, 2011 - iopscience.iop.org
The intrinsic stochasticity of gene expression can lead to large variability in protein levels for
genetically identical cells. Such variability in protein levels can arise from infrequent …

Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing

JC Davis-Turak, K Allison, MN Shokhirev… - Nucleic acids …, 2015 - academic.oup.com
When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control
based on transcription dynamics is widely recognized. Indeed, perturbation studies have …

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

A Honkela, J Peltonen, H Topa… - Proceedings of the …, 2015 - National Acad Sciences
Genes with similar transcriptional activation kinetics can display very different temporal
mRNA profiles because of differences in transcription time, degradation rate, and RNA …

Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing

T Horn, A Gosliga, C Li, M Enculescu… - npj Systems Biology and …, 2023 - nature.com
Alternative splicing is an important step in eukaryotic mRNA pre-processing which increases
the complexity of gene expression programs, but is frequently altered in disease. Previous …

Stochasticity of gene products from transcriptional pulsing

S Iyer-Biswas, F Hayot, C Jayaprakash - Physical Review E—Statistical …, 2009 - APS
Transcriptional pulsing has been observed in both prokaryotes and eukaryotes and plays a
crucial role in cell-to-cell variability of protein and mRNA numbers. An important issue is how …

Stochastic steady state gain in a gene expression process with mRNA degradation control

H Kuwahara, R Schwartz - Journal of the Royal Society …, 2012 - royalsocietypublishing.org
Recent analyses with high-resolution single-molecule experimental methods have shown
highly irregular and variable bursting of mRNA in a wide range of organisms. Noise in gene …

Special function methods for bursty models of transcription

G Gorin, L Pachter - Physical Review E, 2020 - APS
We explore a Markov model used in the analysis of gene expression, involving the bursty
production of pre-mRNA, its conversion to mature mRNA, and its consequent degradation …

Gene transcription in bursting: a unified mode for realizing accuracy and stochasticity

Y Wang, T Ni, W Wang, F Liu - Biological Reviews, 2019 - Wiley Online Library
There is accumulating evidence that, from bacteria to mammalian cells, messenger RNAs
(mRNAs) are produced in intermittent bursts–a much 'noisier'process than traditionally …