ArticlePLoS computational biology2021
Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A conserved coupling of transcriptional ON and OFF periods underlies bursting dynamics.Nature structural & molecular biology · 2025Article
- Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Real-time single-molecule imaging of transcriptional regulatory networks in living cells.Nature reviews. Genetics · 2024Review
- Molecular Crowding: The History and Development of a Scientific Paradigm.Chemical reviews · 2024Review
- Deciphering a global source of non-genetic heterogeneity in cancer cells.Nucleic acids research · 2023Article
- Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology.Cell systems · 2023Article
- Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient.Cell systems · 2023Article
- Gene expression model inference from snapshot RNA data using Bayesian non-parametrics.Nature computational science · 2023Article
- STREAMING-Tag System: Technology to Enable Visualization of Transcriptional Activity and Subnuclear Localization of Specific Endogenous Genes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity.Nature communications · 2022Article
- Article
- Collective polymerase dynamics emerge from DNA supercoiling during transcription.Biophysical journal · 2022Article
- Notch-dependent and -independent transcription are modulated by tissue movements at gastrulation.eLife · 2022Article
- Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number.Science advances · 2022Article
- Application of Domain- and Genotype-Specific Models to Infer Post-Transcriptional Regulation of Segmentation Gene Expression inLife (Basel, Switzerland) · 2021Article
- Live imaging and quantitation of nascent transcription using the MS2/MCP system in theSTAR protocols · 2021Article
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7 authors.
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Abstract
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 well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.
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