Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons
Open accessAbstract
Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ∼3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.
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Inhibition of P-TEFb and thus repression of the release of RNA Pol II from promoter-proximal pausing blocks transcription of almost all genes.
“Inhibition of P‐TEFb and thus repression of the release of RNA Pol II from promoter‐proximal pausing has been shown to block transcription of almost all genes (Henriques et al, 2013; Jonkers et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The Results section, “P-TEFb dependent escape from the pause occurs at all active TSSs,” reports reduced Pol II density downstream of the TSS in 95% of the actively transcribed genes measured after P-TEFb inhibition. The paper supports a block in entry into productive elongation, but not a block of all transcription: it says initiation and early elongation can continue, and its 95% finding is limited to actively transcribed genes. (LLM, conf=0.84)
Experimental — accuracy not yet measuredRNA Pol II speed is highly variable within individual genes, as RNA Pol II accelerates while traveling throughout the gene body, starting at 0.5 kb/min in the first 10-15 kb and accelerating up to 2-4 kb/min downstream.
“RNA Pol II speed was furthermore also shown to be highly variable within individual genes, as RNA Pol II accelerates while traveling throughout the gene body, starting at 0.5 kb/min in the first 10–15 kb and accelerating up to 2–4 kb/min downstream (Danko et al, 2013; Fuchs et al, 2014b; Jonkers et al, 2014; Saponaro et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The Results sections on measuring elongation and independently confirming acceleration report that Pol II speeds increase within most individual genes; mean early and late rates were 0.5 and 2.4 kb/min. The Discussion reports measured rates spanning 0.5–4 kb/min, but the copy does not place the 0.5 kb/min rate specifically in the first 10–15 kb or establish 2–4 kb/min as the downstream range. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIn mammals and many other metazoans, promoter-proximal pausing occurs 25-50 base pairs downstream from the TSS and is a major rate-limiting step of the transcription cycle.
“In mammals and many other metazoans, promoter‐proximal pausing occurs 25–50 base pairs downstream from the TSS and is a major rate‐limiting step of the transcription cycle (Jonkers et al, 2014; Mayer et al, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The Introduction (page unavailable) describes promoter-proximal pausing as potentially rate-limiting and places it +20 to 100 nucleotides downstream of the TSS. The Discussion (page unavailable) calls escape from pausing an integral step in the transcription cycle. The copy does not establish the narrower 25–50-base-pair range or the claim's scope across many other metazoans. (LLM, conf=0.86)
Experimental — accuracy not yet measuredGenome-wide techniques showed in various human cell lines that average RNA Pol II speed ranges between 1.25 kb/min and 3.5 kb/min.
“All these techniques showed in various human cell lines that the average RNA Pol II speed ranges between 1.25 kb/min and 3.5 kb/min (Danko et al, 2013; Fuchs et al, 2014b; Jonkers et al, 2014; Saponaro et al, 2014; Veloso et al, 2014; Liang et al, 2018; Baluapuri et al, 2019; Gregersen et al, 2020).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The Results section, “Measuring the speed of elongating Pol II in the gene body” (page unavailable), reports genome-wide measurements and average rates of 0.5, 1.8, and 2.4 kb/min for three measurement intervals. The Methods section, “Cell culture, nuclei isolation and GRO-seq library preparation” (page unavailable), identifies the cells as mouse embryonic stem cells. This paper therefore supports the general point that a genome-wide technique measured Pol II speed, but not the stated 1.25–3.5 kb/min range in human cell lines. (LLM, conf=0.88)
Experimental — accuracy not yet measuredNo general correlation has been found between nucleosome occupancy and RNA Pol II speed.
“Although no general correlation has been found between nucleosome occupancy and RNA Pol II speed (Jonkers et al, 2014), nucleosomes bound within exons could nonetheless slow down RNA Pol II transcription.”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The Results section (‘Determinants of the elongation rates’; page unavailable) says gene-body elongation rate is unaffected by nucleosome occupancy, supporting the claim in that context. But it also reports that a wider nucleosome-free region at promoters correlates with faster downstream elongation, so the unqualified statement is broader than the paper supports. (LLM, conf=0.85)
Experimental — accuracy not yet measured
GC content within gene bodies correlates negatively with RNA Pol II speed.
“Moreover, the GC content within gene bodies has been shown to correlate negatively with RNA Pol II speed (Jonkers et al, 2014; Veloso et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The Results section (“Determinants of the elongation rates”) reports a modest negative correlation between gene-body CG dinucleotide density and Pol II elongation rate. The cited passage does not establish the same correlation for overall GC content, which is a different measure. (LLM, conf=0.86)
Experimental — accuracy not yet measuredH3K79me2, H2B mono-ubiquitylation, and H4K20me1 positively correlate with RNA Pol II speed in the gene body.
“Genome‐wide studies have shown that H3K79me2, H2B mono‐ubiquitylation, and H4K20me1 positively correlate with RNA Pol II speed in the gene body (Fuchs et al, 2014a; Jonkers et al, 2014; Veloso et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The Results section ('Determinants of the elongation rates'; page not provided) reports that H3K79me2 is enriched in faster genes, supporting its positive association with Pol II elongation rate. Our copy does not establish the claimed positive correlations for H2B mono-ubiquitylation or H4K20me1; searches for those marks and their alternative names found no supporting passages. (LLM, conf=0.87)
Experimental — accuracy not yet measuredFast transcription correlates with distal localization of H3K36me3.
“Indeed, fast transcription correlates with distal localization of H3K36me3 (Jonkers et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
Genes with the highest measured RNA Pol II velocity generate more mRNAs.
“Indeed, genes with the highest measured RNA Pol II velocity have been shown to generate more mRNAs (Danko et al, 2013; Jonkers et al, 2014; Cohen et al, 2018).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
A positive correlation has been identified between intron 1 size and RNA Pol II speed.
“Indeed, a positive correlation has been identified between intron 1 size and RNA Pol II speed (Jonkers et al, 2014)”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
Exon density correlates negatively with RNA Pol II velocity.
“Conversely, exon density correlates negatively with RNA Pol II velocity (Jonkers et al, 2014; Veloso et al, 2014)”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
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- Authors
- Jonkers, I., Kwak, H., & Lis, J. T.
- Affiliations
- Cornell University (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Jonkers, Iris
- Lis, John T
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2014-04-29
- Volume
- 3
- Pages
- e02407-e02407
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC4001325
- OpenAlex
- W2038894647
- Cited by
- 581
- References
- 67
- Citations by year
- 2026: 26 · 2025: 40 · 2024: 52 · 2023: 48 · 2022: 46 · 2021: 74 · 2020: 40 · 2019: 57 · 2018: 53 · 2017: 53 · 2016: 49 · 2015: 35 · 2014: 8
- FWCI
- 19.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- Funders
- National Institutes of Health (GM25232)
- Helen Hay Whitney Foundation
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- RNA polymerase II elongation, promoter-proximal pausing, transcription kinetics, mouse embryonic stem cells, triptolide, flavopiridol, GRO-seq, H3K79me2, chromatin
- MeSH terms
- Animals, Cells, Cultured, Chromatin, Diterpenes, Epoxy Compounds, Exons, Flavonoids, Humans, Phenanthrenes, Piperidines, Promoter Regions, Genetic, RNA Polymerase II, RNA, Messenger, Transcription, Genetic, Genetic Variation, Gene Library, Sequence Alignment, Sequence Analysis, DNA, Chromatin Immunoprecipitation, Mice, Embryonic Stem Cells, Genetic Association Studies
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