ArticleMethods in enzymology2016
Fluctuation Analysis: Dissecting Transcriptional Kinetics with Signal Theory.
Article in Methods in enzymology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- REAL-TIME VISUALIZATION OF SPLICEOSOME ASSEMBLY REVEALS BASIC PRINCIPLES OF 3' SPLICE SITE SELECTION.Research square · 2026Article
- UTag, a cysteine-free thermostable tagging system for tracking single mRNA translation live.Research square · 2026Article
- UTag, a cysteine-free thermostable tagging system for tracking single mRNA translation live.bioRxiv : the preprint server for biology · 2026Article
- U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs.Molecular cell · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- MicroLive: an image processing toolkit for quantifying live-cell single-molecule microscopy.Bioinformatics advances · 2026Article
- MicroLive: An Image Processing Toolkit for Quantifying Live-cell Single-Molecule Microscopy.bioRxiv : the preprint server for biology · 2025Article
- Coordinated active repression operates via transcription factor cooperativity and multiple inactive promoter states in a developing organism.Nature communications · 2025Article
- All Probes Plasmids (APPs) for multicolor and long-term tracking of single-mRNA translation dynamics.Molecular biology of the cell · 2025Article
- Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription.Nature communications · 2024Article
- REAL-TIME VISUALIZATION OF SPLICEOSOME ASSEMBLY REVEALS BASIC PRINCIPLES OF SPLICE SITE SELECTION.bioRxiv : the preprint server for biology · 2024Article
- Translation Dynamics of Single mRNAs in Live Cells.Annual review of biophysics · 2024Review
- BurstDECONV: a signal deconvolution method to uncover mechanisms of transcriptional bursting in live cells.Nucleic acids research · 2023Article
- Transcriptional bursting: stochasticity in deterministic development.Development (Cambridge, England) · 2023Review
- Using Mechanistic Models and Machine Learning to Design Single-Color Multiplexed Nascent Chain Tracking Experiments.bioRxiv : the preprint server for biology · 2023Article
- Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments.Frontiers in cell and developmental biology · 2023Article
- STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity.Nature communications · 2022Article
- Eukaryotic gene regulation at equilibrium, or non?Current opinion in systems biology · 2022Article
- Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics.Nature communications · 2021Article
- Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting.Nature communications · 2021Article
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2 authors.
Funding
Abstract
Recent live-cell microscopy techniques now allow the visualization in multiple colors of RNAs as they are transcribed on genes of interest. Following the number of nascent RNAs over time at a single locus reveals complex fluctuations originating from the underlying transcriptional kinetics. We present here a technique based on concepts from signal theory-called fluctuation analysis-to analyze and interpret multicolor transcriptional time traces and extract the temporal signatures of the underlying mechanisms. The principle is to generate, from the time traces, a set of functions called correlation functions. We explain how to compute these functions practically from a set of experimental traces and how to interpret them through different theoretical and computational means. We also present the major difficulties and pitfalls one might encounter with this technique. This approach is capable of extracting mechanistic information hidden in transcriptional fluctuations at multiple timescales and has broad applications for understanding transcriptional kinetics.
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