ArticleGenome research2014
Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 papers.
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Who cites it
190 citing papers in PubMed.
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- Hierarchical interplay between H3K27ac and H3K4me3 in transcriptional regulation.Nature communications · 2026Article
- Collective RNAP Dynamics Link Transcriptional Strength to Fidelity.The journal of physical chemistry letters · 2026Article
- DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID.Nature communications · 2026Article
- Decoding exonic intron retention from sequence: an exploratory study in the human genome.Frontiers in bioinformatics · 2026Article
- Histone methyltransferase DOT1L maintains cell state and restricts cytotoxic potential of CD8 T cells.Science advances · 2025Article
- Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates.Genome research · 2025Article
- DOT1L as a Therapeutic Target: Insights into Epigenetic Regulation and Cancer Treatment.Biomolecules & therapeutics · 2025Review
- Paused RNA polymerase primes promoters via RNA-mediated stabilisation of transcription factor ERα.Nature communications · 2025Article
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
- CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts.bioRxiv : the preprint server for biology · 2025Article
- Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-cell Acute Lymphoblastic Leukemia.Genomics, proteomics & bioinformatics · 2025Article
- ZmSSRP1 facilitates the progression of RNA polymerase II and is essential for kernel development in maize.The Plant cell · 2025Article
- Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs.Molecular cell · 2025Article
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- Histone H4 lysine 20 monomethylation is not a mark of transcriptional silencers.bioRxiv : the preprint server for biology · 2025Article
- Philosophical and distinct SLE epitomes: dogmas in conflict with evidences and an intellectual dissonance between established pathophysiological models.Frontiers in immunology · 2025Review
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
130 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 individual genes in human cells. This technique, BruDRB-seq, revealed gene-specific differences in elongation rates with a median rate of around 1.5 kb/min. We found that genes with rapid elongation rates showed higher densities of H3K79me2 and H4K20me1 histone marks compared to slower elongating genes. Furthermore, high elongation rates had a positive correlation with gene length, low complexity DNA sequence, and distance from the nearest active transcription unit. Features that negatively correlated with elongation rate included the density of exons, long terminal repeats, GC content of the gene, and DNA methylation density in the bodies of genes. Our results suggest that some static gene features influence transcription elongation rates and that cells may alter elongation rates by epigenetic regulation. The BruDRB-seq technique offers new opportunities to interrogate mechanisms of regulation of transcription elongation.
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