ArticleNature protocols2015
Simultaneous measurement of genome-wide transcription elongation speeds and rates of RNA polymerase II transition into active elongation with 4sUDRB-seq.
Article in Nature protocols, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Targeting super elongation complex-driven RNA polymerase II elongation reduces plaque vulnerability.Signal transduction and targeted therapy · 2026Article
- A-to-I edited SNHG3 promotes non-small cell lung cancer metastasis by promoting fatty acid oxidation and resisting ferroptosis.Communications biology · 2025Article
- NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization.International journal of molecular sciences · 2025Article
- Multi Omics Applications in Biological Systems.Current issues in molecular biology · 2024Review
- Article
- A selective and sensitive detection system for 4-thiouridine modification in RNA.RNA (New York, N.Y.) · 2023Article
- Approach to Measuring the Effect of PARP1 on RNA Polymerase II Elongation Rates.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- Timing RNA polymerase pausing with TV-PRO-seq.Cell reports methods · 2021Article
- FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.Molecular cell · 2021Article
- RNA polymerase II speed: a key player in controlling and adapting transcriptome composition.The EMBO journal · 2021Review
- Fast and furious: insights of back splicing regulation during nascent RNA synthesis.Science China. Life sciences · 2021Review
- A heat shock-responsive lncRNAProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling.Genome research · 2020Article
- Using TTNature protocols · 2020Article
- Methods for the analysis of transcriptome dynamics.Toxicology research · 2019Review
- A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes.The EMBO journal · 2019Article
- Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity.Journal of visualized experiments : JoVE · 2018Article
- Pre-mRNA modifications and their role in nuclear processing.Quantitative biology (Beijing, China) · 2018Article
- Solid phase chemistry to covalently and reversibly capture thiolated RNA.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
4sUDRB-seq separately measures, on a genomic scale, the distinct contributions of transcription elongation speed and rate of RNA polymerase II (Pol II) transition into active elongation (TAE) to the overall mRNA production rate. It uses reversible inhibition of transcription elongation with 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB), combined with a pulse of 4-thiouridine (4sU), to tag newly transcribed RNA. After DRB removal, cells are collected at several time points, and tagged RNA is biotinylated, captured on streptavidin beads and sequenced. 4sUDRB-seq enables the comparison of elongation speeds between different developmental stages or different cell types, and it allows the impact of specific transcription factors on transcription elongation speed versus TAE to be studied. RNA preparation takes ∼4 d to complete, with deep sequencing requiring an additional ∼4-11 d plus 1-3 d for bioinformatics analysis. The experimental protocol requires basic molecular biology skills, whereas data analysis requires knowledge in bioinformatics, particularly MATLAB and the Linux environment.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.