Organization and regulation of gene transcription

The elemental mechanism of transcriptional pausing

(2019) Jason Saba et al.   eLife

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors

(2019) Haruhiko Ehara et al.   SCIENCE

Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

(2019) Sreejith J. Nair et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The role of transcription in shaping the spatial organization of the genome

(2019) Bas van Steensel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The C-Terminal Domain of RNA Polymerase II Is a Multivalent Targeting Sequence that Supports Drosophila Development with Only Consensus Heptads

(2019) Feiyue Lu et al.   MOLECULAR CELL

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D

(2019) Michael I. Robson et al.   MOLECULAR CELL

How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes

(2019) Oleksandr Dergai et al.   TRENDS IN GENETICS

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Transcriptional Control by Premature Termination: A Forgotten Mechanism

(2019) Kinga Kamieniarz-Gdula et al.   TRENDS IN GENETICS

Regulation of RNA Polymerase I TranscriptioninDevelopment, Disease, and Aging

(2018) Samim Sharifi et al.   Annual Review of Biochemistry

A Solid-State Conceptualization of Information Transfer from Gene to Message to Protein

(2018) Masato Kato et al.   Annual Review of Biochemistry

Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II

(2018) Christoph Engel et al.   Annual Review of Biophysics

Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators

(2018) Jin Young Kang et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Structural Basis for NusA Stabilized Transcriptional Pausing

(2018) Xieyang Guo et al.   MOLECULAR CELL

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

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

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

Who's In and Who's Out—Compositional Control of Biomolecular Condensates

(2018) Jonathon A. Ditlev et al.   JOURNAL OF MOLECULAR BIOLOGY

A Cdk9–PP1 switch regulates the elongation–termination transition of RNA polymerase II

(2018) Pabitra K. Parua et al.   NATURE

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

Structural basis of RNA polymerase III transcription initiation

(2018) Guillermo Abascal-Palacios et al.   NATURE

Molecular mechanism of promoter opening by RNA polymerase III

(2018) Matthias K. Vorländer et al.   NATURE

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Structural basis of mitochondrial transcription

(2018) Hauke S. Hillen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Promoter Distortion and Opening in the RNA Polymerase II Cleft

(2018) Christian Dienemann et al.   MOLECULAR CELL

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers

(2018) Jacob M. Tome et al.   NATURE GENETICS

Structural basis of the nucleosome transition during RNA polymerase II passage

(2018) Tomoya Kujirai et al.   SCIENCE

Structure of transcribing RNA polymerase II-nucleosome complex

(2018) Lucas Farnung et al.   Nature Communications

The punctilious RNA polymerase II core promoter

(2017) Long Vo ngoc et al.   GENES & DEVELOPMENT

Transcription Factor–Mediator Interfaces: Multiple and Multi-Valent

(2017) Dylan J. Taatjes   JOURNAL OF MOLECULAR BIOLOGY

Transcription without XPB Establishes a Unified Helicase-Independent Mechanism of Promoter Opening in Eukaryotic Gene Expression

(2017) Sergey Alekseev et al.   MOLECULAR CELL

Structures of transcription pre-initiation complex with TFIIH and Mediator

(2017) S. Schilbach et al.   NATURE

Core Mediator structure at 3.4 Å extends model of transcription initiation complex

(2017) Kayo Nozawa et al.   NATURE

A heterochromatin-dependent transcription machinery drives piRNA expression

(2017) Peter Refsing Andersen et al.   NATURE

Mediator structure and rearrangements required for holoenzyme formation

(2017) Kuang-Lei Tsai et al.   NATURE

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

(2017) Lydia Herzel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

(2017) Carrie Bernecky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin-remodeling for transcription

(2017) Yahli Lorch et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Structure of the complete elongation complex of RNA polymerase II with basal factors

(2017) Haruhiko Ehara et al.   SCIENCE

Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation

(2017) S. Branden Van Oss et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Mediator Complex: At the Nexus of RNA Polymerase II Transcription

(2017) Célia Jeronimo et al.   TRENDS IN CELL BIOLOGY

Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

(2017) Carrie Bernecky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I

(2017) Yan Han et al.   eLife

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

(2017) Sofia Battaglia et al.   eLife

A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription

(2017) Matthew A Sdano et al.   eLife

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Mechanisms of Bacterial Transcription Termination: All Good Things Must End

(2016) Ananya Ray-Soni et al.   Annual Review of Biochemistry

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex

(2016) Philip J. Robinson et al.   CELL

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

Human Mitochondrial Transcription Factor B2 Is Required for Promoter Melting during Initiation of Transcription

(2016) Viktor Posse et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive Identification of RNA-Binding Domains in Human Cells

(2016) Alfredo Castello et al.   MOLECULAR CELL

Structure of RNA polymerase I transcribing ribosomal DNA genes

(2016) Simon Neyer et al.   NATURE

Near-atomic resolution visualization of human transcription promoter opening

(2016) Yuan He et al.   NATURE

Transcription initiation complex structures elucidate DNA opening

(2016) C. Plaschka et al.   NATURE

Structure of promoter-bound TFIID and model of human pre-initiation complex assembly

(2016) Robert K. Louder et al.   NATURE

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Structural basis of transcription activation

(2016) Y. Feng et al.   SCIENCE

Transcription Termination: Variations on Common Themes

(2016) Odil Porrua et al.   TRENDS IN GENETICS

Structure of the initiation-competent RNA polymerase I and its implication for transcription

(2016) Michael Pilsl et al.   Nature Communications

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide

(2015) Fei Chen et al.   GENES & DEVELOPMENT

Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble

(2015) Yuhong Zuo et al.   MOLECULAR CELL

Architecture of the RNA polymerase II–Mediator core initiation complex

(2015) C. Plaschka et al.   NATURE

Molecular structures of unbound and transcribing RNA polymerase III

(2015) Niklas A. Hoffmann et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Imaging RNA Polymerase II transcription sites in living cells

(2014) Martin S Buckley et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor

(2014) Nicholas Kwiatkowski et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Kin28 regulates the transient association of Mediator with core promoters

(2014) Célia Jeronimo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Conserved architecture of the core RNA polymerase II initiation complex

(2014) Wolfgang Mühlbacher et al.   Nature Communications

The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1

(2014) Peter J Skene et al.   eLife

Control of Transcriptional Elongation

(2013) Hojoong Kwak et al.   Annual Review of Genetics

Chromatin and DNA sequences in defining promoters for transcription initiation

(2013) Ferenc Müller et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

(2013) Andreas H. Ehrensberger et al.   CELL

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

Global Regulation of Promoter Melting in Naive Lymphocytes

(2013) Fedor Kouzine et al.   CELL

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

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

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

In vivo live imaging of RNA polymerase II transcription factories in primary cells

(2013) A. Ghamari et al.   GENES & DEVELOPMENT

RNA polymerase I structure and transcription regulation

(2013) Christoph Engel et al.   NATURE

Crystal structure of the 14-subunit RNA polymerase I

(2013) Carlos Fernández-Tornero et al.   NATURE

The architecture of human general transcription factor TFIID core complex

(2013) Christoph Bieniossek et al.   NATURE

Structural visualization of key steps in human transcription initiation

(2013) Yuan He et al.   NATURE

Structure of human mitochondrial RNA polymerase elongation complex

(2013) Kathrin Schwinghammer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone chaperone FACT action during transcription through chromatin by RNA polymerase II

(2013) F.-K. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

Nucleosome Remodeling and Epigenetics

(2013) P. B. Becker et al.   Cold Spring Harbor Perspectives in Biology

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

Odd RNA polymerases or the A(B)C of eukaryotic transcription

(2012) André Sentenac et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Structural basis of transcription elongation

(2012) Fuensanta W. Martinez-Rucobo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Regulation of pol III transcription by nutrient and stress signaling pathways

(2012) Robyn D. Moir et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Transcription elongation factors DSIF and NELF: Promoter-proximal pausing and beyond

(2012) Yuki Yamaguchi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries

(2012) Alessandro Vannini et al.   MOLECULAR CELL

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex

(2012) Sarah Sainsbury et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening

(2012) Sebastian Grünberg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

(2012) Michaela Smolle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptional regulation by coactivators in embryonic stem cells

(2012) Yick W. Fong et al.   TRENDS IN CELL BIOLOGY

Structural Basis for Promoter −10 Element Recognition by the Bacterial RNA Polymerase σ Subunit

(2011) Andrey Feklistov et al.   CELL

A history of TFIIH: Two decades of molecular biology on a pivotal transcription/repair factor

(2011) Jean-Marc Egly et al.   DNA REPAIR

Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth

(2011) C. Blattner et al.   GENES & DEVELOPMENT

The super elongation complex (SEC) and MLL in development and disease

(2011) E. Smith et al.   GENES & DEVELOPMENT

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Structural basis of RNA polymerase II backtracking, arrest and reactivation

(2011) Alan C. M. Cheung et al.   NATURE

XPB, a subunit of TFIIH, is a target of the natural product triptolide

(2011) Denis V Titov et al.   Nature Chemical Biology

Evolution of multisubunit RNA polymerases in the three domains of life

(2011) Finn Werner et al.   NATURE REVIEWS MICROBIOLOGY

Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing

(2011) Jeremy R. Haag et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Yeast Rrn7 and Human TAF1B Are TFIIB-Related RNA Polymerase I General Transcription Factors

(2011) B. A. Knutson et al.   SCIENCE

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

HIV-1 Tat Assembles a Multifunctional Transcription Elongation Complex and Stably Associates with the 7SK snRNP

(2010) Bijan Sobhian et al.   MOLECULAR CELL

RNA Polymerase Active Center: The Molecular Engine of Transcription

(2009) Evgeny Nudler   Annual Review of Biochemistry

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

Shifting Players and Paradigms in Cell-Specific Transcription

(2009) Joseph A. D'Alessio et al.   MOLECULAR CELL

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

RNA polymerase II–TFIIB structure and mechanism of transcription initiation

(2009) Dirk Kostrewa et al.   NATURE

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Structure of an RNA Polymerase II-TFIIB Complex and the Transcription Initiation Mechanism

(2009) X. Liu et al.   SCIENCE

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation

(2008) Florian Brueckner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA polymerases I and III, non-coding RNAs and cancer

(2008) Robert J. White   TRENDS IN GENETICS