Modeling bursty transcription and splicing with the chemical master equation
Splicing cascades that alter gene products posttranscriptionally also affect expression
dynamics. We study a class of processes and associated distributions that emerge from …
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 …
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
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 …
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 …
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 …
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 …
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 …
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 …
highly irregular and variable bursting of mRNA in a wide range of organisms. Noise in gene …
Special function methods for bursty models of transcription
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 …
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
There is accumulating evidence that, from bacteria to mammalian cells, messenger RNAs
(mRNAs) are produced in intermittent bursts–a much 'noisier'process than traditionally …
(mRNAs) are produced in intermittent bursts–a much 'noisier'process than traditionally …