Rapid Rates of Pol II Elongation in the Drosophila Embryo
Open accessAbstract
Elongation of RNA polymerase II (Pol II) is thought to be an important mechanism for regulating gene expression [1]. We measured the first wave of de novo transcription in living Drosophila embryos using dual-fluorescence detection of nascent transcripts containing 5' MS2 and 3' PP7 RNA stem loops. Pol II elongation rates of 2.4-3.0 kb/min were observed, approximately twice as fast as earlier estimates [2-6]. The revised rates permit substantial levels of zygotic gene activity prior to the mid-blastula transition. We also provide evidence that variable rates of elongation are not a significant source of differential gene activity, suggesting that transcription initiation and Pol II release are the key determinants of gene control in development.
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Using constructs carrying arrays of MS2 and PP7 repeats in the 5′ and 3′ regions of the same gene, RNA Pol II speed was estimated to range from 0.84 kb/min to 3.66 kb/min.
“By using constructs carrying arrays of MS2 and PP7 repeats in the 5′ and 3′ regions of the same gene, RNA Pol II speed was estimated to range from 0.84 kb/min to 3.66 kb/min (Hocine et al, 2013; Fukaya et al, 2017).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Fukaya et al, 2017
The Results and Discussion describe a reporter gene with 5′ MS2 and 3′ PP7 repeats, used to estimate Pol II elongation speed. But the paper reports rates of 2.4–3.0 kb/min in early Drosophila embryos, not the attributed range of 0.84–3.66 kb/min. Page numbers are unavailable in our copy. (LLM, conf=0.90)
Experimental — accuracy not yet measuredThe presence of introns increases transcription speed.
“and the presence of introns increases transcription speed (Fukaya et al, 2017).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Fukaya et al, 2017
In Results and Discussion, the intron-containing yellow reporter showed approximately 20% faster Pol II elongation than intron-less lacZ. The authors explicitly say they cannot exclude DNA sequence features, rather than the intron, as the cause, so the citation does not establish the claim as stated. (LLM, conf=0.88)
Experimental — accuracy not yet measuredRNA Pol II velocity has been suggested to affect the timing of mRNA accumulation and could thus play a role in the timing of some developmental regulatory processes.
“Nevertheless, RNA Pol II velocity has also been suggested to affect the timing of mRNA accumulation and could thus play a role in the timing of some developmental regulatory processes (Thummel et al, 1990; Fukaya et al, 2017; Maslon et al, 2019).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Fukaya et al, 2017
Other studies have found no relationship between RNA Pol II speed and expression levels.
“However, other studies have found no relationship between RNA Pol II speed and expression levels (Singh & Padgett, 2009; Fukaya et al, 2017).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Fukaya et al, 2017
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Self-citationNewly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent StatesPreprint
Shao, R., Kumar, B., Lidschreiber, K., Lidschreiber, M., Cramer, P., & Elsässer, S. (2021) · bioRxiv · doi:10.1101/2021.06.11.448016
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Defining Kinetic Roles of Transcriptional Activators in the Early Drosophila EmbryoPreprint
Harden, T. T., Vincent, B. J., & DePace, A. H. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3806071
Deng, H., & Lim, B. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.16.456541
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Opticool: Cutting-edge transgenic optical tools
Fenelon, K. D., Krause, J., & Koromila, T. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011208
Ma, M., & Grima, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.02.673499
Decoding the impact of promoter sequences on transcriptional dynamics in vivo
Oliveros, K. C. F. (2019) · theses.fr (ABES) · doi:10.70675/ae0abf40z0fe4z4445zaea9zf5558004f8b9
Real time imaging of transcription reveals new features of cellular and viral promoters
Kozulic-Pirher, A. (2018) · theses.fr (ABES) · doi:10.70675/0099e36bz620ez43d7z9b47z2789ed360d73
Transcription factor clusters enhance gene expression in vivo without modulating bursting dynamics
Cadar, E., Birnie, A., Marsman, R., Grond, R., & Bothma, J. P. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.09.011
- Authors
- Fukaya, T., Lim, B., & Levine, M.
- Affiliations
- Princeton University (US)
- Corresponding author
- Fukaya, Takashi
- Levine, Michael
- Venue
- Current Biology
- Publisher
- Elsevier BV
- Published
- 2017-05
- Volume
- 27
- Issue
- 9
- Pages
- 1387-1391
- ISSN
- 0960-9822 (ISSN-L)
- PMC
- PMC5665007
- OpenAlex
- W2608376949
- Cited by
- 84
- References
- 27
- Citations by year
- 2026: 2 · 2025: 9 · 2024: 5 · 2023: 12 · 2022: 7 · 2021: 16 · 2020: 7 · 2019: 10 · 2018: 15 · 2017: 1
- FWCI
- 3.69
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Current Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Human Frontier Science Program
- National Institutes of Health (1F32GM122186, U01EB021239, GM118147)
- 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 › Developmental Biology and Gene Regulation
- Keywords
- RNA polymerase II elongation, elongation rate, Drosophila embryo, midblastula transition, nascent RNA, transcription initiation, gene expression regulation, embryonic development
- MeSH terms
- Animals, Drosophila, Embryo, Nonmammalian, Female, Gene Expression Regulation, Male, Promoter Regions, Genetic, RNA Polymerase II, Drosophila Proteins, Transcription Initiation, Genetic, Transcription Elongation, Genetic
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