ArticleMolecular systems biology2022
Distinct transcription kinetics of pluripotent cell states.
Article in Molecular systems biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes.bioRxiv : the preprint server for biology · 2026Article
- Graded versus ON/OFF control in quantitative gene expression and epigenetic memory.The EMBO journal · 2026Review
- Antisense transcription can induce expression memory via stable promoter repression.Genome biology · 2025Article
- Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates.Genome research · 2025Article
- Rewired m6A of promoter antisense RNAs in Alzheimer's disease regulates neuronal genes in 3D nucleome.Nature communications · 2025Article
- Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.Nature protocols · 2025Review
- Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting.Molecular systems biology · 2024Article
- DOT1L is a barrier to histone acetylation during reprogramming to pluripotency.Science advances · 2023Article
- Distinct transcription kinetics of pluripotent cell states.Molecular systems biology · 2022Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mouse embryonic stem cells (mESCs) can adopt naïve, ground, and paused pluripotent states that give rise to unique transcriptomes. Here, we use transient transcriptome sequencing (TT-seq) to define both coding and non-coding transcription units (TUs) in these three pluripotent states and combine TT-seq with RNA polymerase II occupancy profiling to unravel the kinetics of RNA metabolism genome-wide. Compared to the naïve state (serum), RNA synthesis and turnover rates are globally reduced in the ground state (2i) and the paused state (mTORi). The global reduction in RNA synthesis goes along with a genome-wide decrease of polymerase elongation velocity, which is related to epigenomic features and alterations in the Pol II termination window. Our data suggest that transcription activity is the main determinant of steady state mRNA levels in the naïve state and that genome-wide changes in transcription kinetics invoke ground and paused pluripotent states.
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