ArticleNucleic acids research2023
Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 50 citations in OpenAlex.
- Deciphering global transcriptional dynamics coordinated by gene-gene regulatory interactions using single-cell data.Molecular systems biology · 2026Article
- Transcriptional Bursting in Pluripotent Stem Cells.Biology · 2026Review
- Cell trajectory inference based on schrödinger problem and a mechanistic model of stochastic gene expression.NPJ systems biology and applications · 2026Article
- Article
- From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq.PLoS computational biology · 2026Article
- Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances.bioRxiv : the preprint server for biology · 2025Article
- The chronODE framework for modelling multi-omic time series with ordinary differential equations and machine learning.Nature communications · 2025Article
- Genetic characteristics of novel extreme alkaline-inducible promoter located in five prime upstream region of peptidyl-prolyl cis/trans isomerase from Vibrio anguillarum.Scientific reports · 2025Article
- Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives.PLoS computational biology · 2025Article
- Efficient approximations of transcriptional bursting effects on the dynamics of a gene regulatory network.Journal of the Royal Society, Interface · 2025Article
- Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data.Nucleic acids research · 2025Article
- Marker genes reveal dynamic features of cell evolving processes.Bioinformatics advances · 2025Article
- KSRV: a Kernel PCA-Based framework for inferring spatial RNA velocity at single-cell resolution.Frontiers in genetics · 2025Article
- Advancements in single-cell RNA sequencing and spatial transcriptomics: transforming biomedical research.Acta biochimica Polonica · 2025Review
- Genetically Encoded Trensor Circuits Report HeLa Cell Treatment with Polyplexed Plasmid DNA and Small-Molecule Transfection Modulators.ACS synthetic biology · 2024Article
- Stochastic Gene Expression in Proliferating Cells: Differing Noise Intensity in Single-Cell and Population Perspectives.bioRxiv : the preprint server for biology · 2024Article
- Decoding the principle of cell-fate determination for its reverse control.NPJ systems biology and applications · 2024Article
- What can we learn when fitting a simple telegraph model to a complex gene expression model?PLoS computational biology · 2024Article
- Quantifying and correcting bias in transcriptional parameter inference from single-cell data.Biophysical journal · 2024Article
- Transcriptional bursting dynamics in gene expression.Frontiers in genetics · 2024Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 architecture and dynamic feedback regulations dictate bursting on a genome-wide scale. Although single-cell RNA sequencing (scRNA-seq) provides an opportunity to address this challenge, effective analytical methods are scarce. We developed an interpretable and scalable inference framework, which combined experimental data with a mechanistic model to infer transcriptional burst kinetics (sizes and frequencies) and feedback regulations. Applying this framework to scRNA-seq data generated from embryonic mouse fibroblast cells, we found Simpson's paradoxes, i.e. genome-wide burst kinetics exhibit different characteristics in two cases without and with distinguishing feedback regulations. We also showed that feedbacks differently modulate burst frequencies and sizes and conceal the effects of transcription start site distributions on burst kinetics. Notably, only in the presence of positive feedback, TATA genes are expressed with high burst frequencies and enhancer-promoter interactions mainly modulate burst frequencies. The developed inference method provided a flexible and efficient way to investigate transcriptional burst kinetics and the obtained results would be helpful for understanding cell development and fate decision.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.