ArticleNature cell biology2024
Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts.
Article in Nature cell biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- The molecular basis of transcription initiation by RNA polymerase II.Nature reviews. Molecular cell biology · 2026Review
- 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
- Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis.bioRxiv : the preprint server for biology · 2026Article
- Stochastic Gene Expression Model with State-Dependent Protein Activation Delay.bioRxiv : the preprint server for biology · 2026Article
- Predicting Macrophage Spatial Localization from Single-Cell Transcriptomes to Uncover Disease Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq.PLoS computational biology · 2026Article
- High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo.Research square · 2026Article
- High-resolution binding data of TFIID and cofactors show promoter-specific differencesbioRxiv : the preprint server for biology · 2025Article
- Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data.Bioinformatics (Oxford, England) · 2025Article
- Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling.Nature communications · 2025Article
- Uncovering candidate Nanog-Helper genes in early mouse embryo differentiation using differential entropy and network inference.Scientific reports · 2025Article
- Highly sensitive and scalable time-resolved RNA sequencing in single cells with scNT-seq2.bioRxiv : the preprint server for biology · 2025Article
- Efficient profiling of total RNA in single cells with STORM-seq.bioRxiv : the preprint server for biology · 2025Article
- Regulation of RNA polymerase II transcription through re-initiation and bursting.Molecular cell · 2025Review
- Regulation of Transcriptional Bursting and Spatial Patterning in EarlybioRxiv : the preprint server for biology · 2025Article
- Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II.Molecular systems biology · 2025Article
- Decoding stimulus-specific regulation of promoter activity of p53 target genes.Frontiers in cell and developmental biology · 2025Article
- Transcriptome and Temporal Transcriptome Analyses in Single Cells.International journal of molecular sciences · 2024Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analyses of transcriptional bursting from single-cell RNA-sequencing data have revealed patterns of variation and regulation in the kinetic parameters that could be inferred. Here we profiled newly transcribed (4-thiouridine-labelled) RNA across 10,000 individual primary mouse fibroblasts to more broadly infer bursting kinetics and coordination. We demonstrate that inference from new RNA profiles could separate the kinetic parameters that together specify the burst size, and that the synthesis rate (and not the transcriptional off rate) controls the burst size. Importantly, transcriptome-wide inference of transcriptional on and off rates provided conclusive evidence that RNA polymerase II transcribes genes in bursts. Recent reports identified examples of transcriptional co-bursting, yet no global analyses have been performed. The deep new RNA profiles we generated with allelic resolution demonstrated that co-bursting rarely appears more frequently than expected by chance, except for certain gene pairs, notably paralogues located in close genomic proximity. Altogether, new RNA single-cell profiling critically improves the inference of transcriptional bursting and provides strong evidence for independent transcriptional bursting of mammalian genes.
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