Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces

Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA

(2020) Rafal Donczew et al.   eLife

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker’s yeast

(2019) William R. Blevins et al.   Scientific Reports

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Widespread and precise reprogramming of yeast protein–genome interactions in response to heat shock

(2018) Vinesh Vinayachandran et al.   GENOME RESEARCH

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II

(2018) Barbara Steurer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transient pausing by RNA polymerase II

(2018) David H. Price   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simplified ChIP-exo assays

(2018) Matthew J. Rossi et al.   Nature Communications

Transcript Buffering: A Balancing Act between mRNA Synthesis and mRNA Degradation

(2018) H.Th. Marc Timmers et al.   MOLECULAR CELL

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters

(2017) Arnaud R. Krebs et al.   MOLECULAR CELL

Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation

(2017) Ameet Shetty et al.   MOLECULAR CELL

Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

(2017) Linda Warfield et al.   MOLECULAR CELL

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning

(2017) Eric J Tomko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome

(2017) Kyle A. Nilson et al.   NUCLEIC ACIDS RESEARCH

TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning

(2017) Eric J Tomko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

(2017) Audrey P. Gasch et al.   PLOS BIOLOGY

RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

(2017) Sofia Battaglia et al.   eLife

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

(2016) Gregory T. Booth et al.   GENOME RESEARCH

Genome-wide uniformity of human ‘open’ pre-initiation complexes

(2016) William K.M. Lai et al.   GENOME RESEARCH

Biochemical Analysis of Yeast Suppressor of Ty 4/5 (Spt4/5) Reveals the Importance of Nucleic Acid Interactions in the Prevention of RNA Polymerase II Arrest

(2016) J. Brooks Crickard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization

(2016) Juan B. Rodríguez-Molina et al.   MOLECULAR CELL

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Molecular mechanisms of ribosomal protein gene coregulation

(2015) Rohit Reja et al.   GENES & DEVELOPMENT

Uncoupling Promoter Opening from Start-Site Scanning

(2015) Kenji Murakami et al.   MOLECULAR CELL

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress

(2015) Antonis Giannakakis et al.   Scientific Reports

The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription

(2014) Jacques Bonnet et al.   GENES & DEVELOPMENT

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

TFIIH Phosphorylation of the Pol II CTD Stimulates Mediator Dissociation from the Preinitiation Complex and Promoter Escape

(2014) Koon Ho Wong et al.   MOLECULAR CELL

Pol II Docking and Pausing at Growth and Stress Genes in C. elegans

(2014) Colin S. Maxwell et al.   Cell Reports

Hydrogen peroxide sensing, signaling and regulation of transcription factors

(2014) H. Susana Marinho et al.   Redox Biology

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

(2013) Mounia Lagha et al.   CELL

The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code

(2013) Célia Jeronimo et al.   CHEMICAL REVIEWS

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

RNA Polymerase II Transcription Elongation Control

(2013) Jiannan Guo et al.   CHEMICAL REVIEWS

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels

(2013) Mai Sun et al.   MOLECULAR CELL

A feed forward circuit comprising Spt6, Ctk1 and PAF regulates Pol II CTD phosphorylation and transcription elongation

(2013) R. Dronamraju et al.   NUCLEIC ACIDS RESEARCH

RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

The COMPASS Family of Histone H3K4 Methylases: Mechanisms of Regulation in Development and Disease Pathogenesis

(2012) Ali Shilatifard   Annual Review of Biochemistry

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

A Universal RNA Polymerase II CTD Cycle Is Orchestrated by Complex Interplays between Kinase, Phosphatase, and Isomerase Enzymes along Genes

(2012) Alain R. Bataille et al.   MOLECULAR CELL

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

The Response to Heat Shock and Oxidative Stress in Saccharomyces cerevisiae

(2011) K. A. Morano et al.   GENETICS

Stable and dynamic nucleosome states during a meiotic developmental process

(2011) L. Zhang et al.   GENOME RESEARCH

Controlling gene expression in response to stress

(2011) Eulàlia de Nadal et al.   NATURE REVIEWS GENETICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Detecting transcriptionally engaged RNA polymerase in eukaryotic cells with permanganate genomic footprinting

(2009) David S. Gilmour et al.   METHODS

Phosphorylation of the Transcription Elongation Factor Spt5 by Yeast Bur1 Kinase Stimulates Recruitment of the PAF Complex

(2009) Y. Liu et al.   MOLECULAR AND CELLULAR BIOLOGY

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

(2009) K. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila

(2008) C. Lee et al.   MOLECULAR AND CELLULAR BIOLOGY