Correction: Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II

The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.

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NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution

10.1101/246827 ◽

2018 ◽

Author(s):

Constantine Mylonas ◽

Peter Tessarz

Keyword(s):

Splicing Factors ◽

Elongation Factors ◽

Single Nucleotide ◽

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide ◽

Regulatory Complexity ◽

Pol Ii Pausing ◽

Nucleotide Resolution ◽

The Impact

ABSTRACTThe advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. However, little is known, at such high resolution, how transcription factors directly influence RNA Pol II pausing and directionality. To map the impact of transcription/elongation factors on transcription dynamics genome-wide at base pair resolution, we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). Application of NET-prism on elongation factors (Spt6, Ssrp1), splicing factors (Sf1), and components of the pre-initiation complex (PIC) (TFIID, and Mediator) reveals their inherent command on transcription dynamics, with regards to directionality and pausing over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity during gene expression.

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Nutrient-Driven O-GlcNAcylation at Promoters Impacts Genome-Wide RNA Pol II Distribution

Frontiers in Endocrinology ◽

10.3389/fendo.2018.00521 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 3

Author(s):

Michael W. Krause ◽

Dona C. Love ◽

Salil K. Ghosh ◽

Peng Wang ◽

Sijung Yun ◽

...

Keyword(s):

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide

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Genome-Wide Mapping of RNA Pol-II Promoter Usage in Mouse Tissues by ChIP-Seq

Methods in Molecular Biology - Cancer Genomics and Proteomics ◽

10.1007/978-1-4939-0992-6_1 ◽

2014 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Sharmistha Pal ◽

Ravi Gupta ◽

Ramana V. Davuluri

Keyword(s):

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide ◽

Mouse Tissues ◽

Promoter Usage ◽

Rna Pol Ii Promoter

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GENOME‐WIDE DISTRIBUTIONS OF RNA POL II CTD PHOSPHORYLATION AND CTD‐ASSOCIATED TERMINATION FACTORS IN BUDDING YEAST

The FASEB Journal ◽

10.1096/fasebj.24.1_supplement.406.1 ◽

2010 ◽

Vol 24 (S1) ◽

Author(s):

David Bentley

Keyword(s):

Budding Yeast ◽

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide ◽

Ctd Phosphorylation

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Regulation of Pol II Pausing Is Involved in Daily Gene Transcription in the Mouse Liver

Journal of Biological Rhythms ◽

10.1177/0748730418779526 ◽

2018 ◽

Vol 33 (4) ◽

pp. 350-362 ◽

Cited By ~ 2

Author(s):

Jialou Zhu ◽

Chengwei Li ◽

Changxia Gong ◽

Xiaodong Li

Keyword(s):

Gene Transcription ◽

Mouse Liver ◽

Phase Distribution ◽

Gene Body ◽

Pol Ii ◽

Genome Wide ◽

A Genome ◽

Pol Ii Pausing ◽

Transcriptional Output

The circadian clock orchestrates gene expression rhythms. Regulation at the level of gene transcription is essential for molecular and cellular rhythms. Pol II pause release is a critical step of transcription regulation. However, whether and how Pol II pause release is regulated during daily transcription have not been characterized. In this study, we performed Pol II ChIP-seq across the day in the mouse liver and quantitatively analyzed binding signals within the transcription start site (TSS) region and the gene body. We frequently found discordant changes between Pol II near the TSS ([Pol II]TSS, paused Pol II) and that within the gene body ([Pol II]GB, transcribing Pol II) across the genome, with only [Pol II]GB always reflecting transcription of clock and clock-controlled genes. Accordingly, Pol II traveling ratios of more than 7000 genes showed significant daily changes (>1.5-fold). Therefore, there is widespread regulation of Pol II pausing in the mouse liver. Interestingly, gene transcription rhythms exhibited a bimodal phase distribution. The transcription of ~400 genes peaked near ZT0, coincident with a genome-wide increase in [Pol II]TSS and traveling ratio (TR). The transcription of ~300 other genes peaked ~12 h later, when there was a global decrease in [Pol II]TSS and TR. ChIP-seq against TATA-binding protein (Tbp), a preinitiation complex (PIC) component, revealed that Pol II recruitment mainly played an indirect role in transcriptional output, with transcriptional termination and pause release functioning prominently in determining the fate of initiated Pol II and its pausing status. Taken together, our results revealed a critical, albeit complex role of Pol II pausing control in regulating the temporal output of gene transcription.

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Genome-wide RNA pol II initiation and pausing in neural progenitors of the rat

BMC Genomics ◽

10.1186/s12864-019-5829-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Adam Scheidegger ◽

Carissa J. Dunn ◽

Ann Samarakkody ◽

Nii Koney-Kwaku Koney ◽

Danielle Perley ◽

...

Keyword(s):

Neural Progenitors ◽

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide

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Selective Requirement for SAGA in Hog1-Mediated Gene Expression Depending on the Severity of the External Osmostress Conditions

Molecular and Cellular Biology ◽

10.1128/mcb.00089-07 ◽

2007 ◽

Vol 27 (11) ◽

pp. 3900-3910 ◽

Cited By ~ 68

Author(s):

Meritxell Zapater ◽

Marc Sohrmann ◽

Matthias Peter ◽

Francesc Posas ◽

Eulàlia de Nadal

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Genetic Screening ◽

Essential Role ◽

Regulation Of Gene Expression ◽

Transcriptional Program ◽

Rna Pol Ii ◽

Pol Ii ◽

Genome Wide ◽

Transcriptional Complex

ABSTRACT Regulation of gene expression by the Hog1 stress-activated protein kinase is essential for proper cell adaptation to osmostress. Hog1 coordinates an extensive transcriptional program through the modulation of transcription. To identify systematically novel components of the transcriptional machinery required for osmostress-mediated gene expression, we performed an exhaustive genome-wide genetic screening, searching for mutations that render cells osmosensitive at high osmolarity and that are associated with reduced expression of osmoresponsive genes. The SAGA and Mediator complexes were identified as putative novel regulators of osmostress-mediated transcription. Interestingly, whereas Mediator is essential for osmostress gene expression, the requirement for SAGA is different depending on the strength of the extracellular osmotic conditions. At mild osmolarity, SAGA mutants show only very slight defects on RNA polymerase II (Pol II) recruitment and gene expression, whereas at severe osmotic conditions, SAGA mutants show completely impaired RNA Pol II recruitment and transcription of osmoresponsive genes. Thus, our results define an essential role for Mediator in osmostress gene expression and a selective role for SAGA under severe osmostress. Our results indicate that the requirement for a transcriptional complex to regulate a promoter might be determined by the strength of the stimuli perceived by the cell through the regulation of interactions between transcriptional complexes.

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