ArticleMolecular systems biology2016
Strand-specific, high-resolution mapping of modified RNA polymerase II.
Article in Molecular systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- CTDP1 governs a Pol II phosphorylation intermediate and coordinates Mediator recruitment, transcription efficiency, and splicing.Nucleic acids research · 2026Article
- Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide.Nucleic acids research · 2025Article
- Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae.Nucleic acids research · 2021Article
- Diverse and conserved roles of the protein Ssu72 in eukaryotes: from yeast to higher organisms.Current genetics · 2021Review
- Transcription shapes genome-wide histone acetylation patterns.Nature communications · 2021Article
- Specific Features of RNA Polymerases I and III: Structure and Assembly.Frontiers in molecular biosciences · 2021Review
- Coupling Between Production of Ribosomal RNA and Maturation: Just at the Beginning.Frontiers in molecular biosciences · 2021Review
- Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates.Molecular cell · 2020Article
- Substrate specificity of the TRAMP nuclear surveillance complexes.Nature communications · 2020Article
- Using TTNature protocols · 2020Article
- Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress.The Plant cell · 2019Article
- Nascent RNA and the Coordination of Splicing with Transcription.Cold Spring Harbor perspectives in biology · 2019Review
- Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome.RNA biology · 2019Article
- Article
- Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination.Cell reports · 2018Article
- A Nuclear Export Block Triggers the Decay of Newly Synthesized Polyadenylated RNA.Cell reports · 2018Article
- Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3' End RNA-Seq.Cell reports · 2018Article
- Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions.Life science alliance · 2018Article
- Surveillance-ready transcription: nuclear RNA decay as a default fate.Open biology · 2018Review
- High-resolution transcription maps reveal the widespread impact of roadblock termination in yeast.The EMBO journal · 2018Article
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Authors and funding
9 authors.
Funding
Abstract
Reversible modification of the RNAPII C-terminal domain links transcription with RNA processing and surveillance activities. To better understand this, we mapped the location of RNAPII carrying the five types of CTD phosphorylation on the RNA transcript, providing strand-specific, nucleotide-resolution information, and we used a machine learning-based approach to define RNAPII states. This revealed enrichment of Ser5P, and depletion of Tyr1P, Ser2P, Thr4P, and Ser7P in the transcription start site (TSS) proximal ~150 nt of most genes, with depletion of all modifications close to the poly(A) site. The TSS region also showed elevated RNAPII relative to regions further 3', with high recruitment of RNA surveillance and termination factors, and correlated with the previously mapped 3' ends of short, unstable ncRNA transcripts. A hidden Markov model identified distinct modification states associated with initiating, early elongating and later elongating RNAPII. The initiation state was enriched near the TSS of protein-coding genes and persisted throughout exon 1 of intron-containing genes. Notably, unstable ncRNAs apparently failed to transition into the elongation states seen on protein-coding genes.
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