ArticleNature2011
Nascent transcript sequencing visualizes transcription at nucleotide resolution.
Article in Nature, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 518 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
518 citing papers in PubMed.
- Esc2 and Rad57 contribute to RNA polymerase II distribution at highly transcribed genes.Life science alliance · 2027Article
- Ionomycin suppresses cancer cell growth by disrupting mitochondrial transcription.FEBS open bio · 2026Article
- Regulation of the histone H3K36 methyltransferase Set2 by the histone chaperone Spt6.Nucleic acids research · 2026Article
- Nucleotide resolution 4-thiouridine sequencing by SNU-Seq and sf4sU-Seq reveals the transcriptional responsiveness of an epigenetically primed human genome.Nucleic acids research · 2026Article
- A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation.bioRxiv : the preprint server for biology · 2026Article
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate.Annual review of biochemistry · 2026Review
- Regulation of the histone H3K36 methyltransferase Set2 by the histone chaperone Spt6.bioRxiv : the preprint server for biology · 2026Article
- KAS-CUT&Tag for direct mapping of transcription bubbles.bioRxiv : the preprint server for biology · 2026Article
- Article
- RNAP-seq:bioRxiv : the preprint server for biology · 2026Article
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- Comprehensive profiling of chromatin occupancy dynamics through the cell cycle.Nucleic acids research · 2026Article
- Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.Genome research · 2026Article
- The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation.RNA biology · 2025Review
- H2A.Z and H3:K56Q Affect Transcription Through Chromatin and Yeast FACT-Dependent Nucleosome Unfolding.International journal of molecular sciences · 2025Article
- Nucleic Acid Sequence Determinants of Transcriptional Pausing by the Human Mitochondrial RNA Polymerase (POLRMT).Biochemistry · 2025Article
- High-resolution Sequencing Reveals that the Paf1 Complex May be a Conserved Transcription Elongation Factor for Eukaryotic RNA Polymerase I.Journal of molecular biology · 2025Article
- Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination.Nature communications · 2025Article
- FACT weakens the nucleosomal barrier to transcription and preserves its integrity by forming a hexasome-like intermediate.Molecular cell · 2025Article
458 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Recent studies of transcription have revealed a level of complexity not previously appreciated even a few years ago, both in the intricate use of post-initiation control and the mass production of rapidly degraded transcripts. Dissection of these pathways requires strategies for precisely following transcripts as they are being produced. Here we present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3' ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that although promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. Our studies also reveal pervasive polymerase pausing and backtracking throughout the body of transcripts. Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements. Thus, nucleosome-induced pausing represents a major barrier to transcriptional elongation in vivo.
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Registered trials
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.