Understanding transcription across scales: From base pairs to chromosomes

On the role of transcription in positioning nucleosomes

(2021) Zhongling Jiang et al.   PLoS Computational Biology

Organization of the Escherichia coli Chromosome by a MukBEF Axial Core

(2020) Jarno Mäkelä et al.   MOLECULAR CELL

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

Beads on a string—nucleosome array arrangements and folding of the chromatin fiber

(2020) Sandro Baldi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain

(2020) Alister Burt et al.   Nature Communications

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

Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome

(2020) Evan J Worden et al.   eLife

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Stepwise Promoter Melting by Bacterial RNA Polymerase

(2020) James Chen et al.   MOLECULAR CELL

DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

(2020) Vishal Nanavaty et al.   MOLECULAR CELL

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

(2020) Svetlana O. Dodonova et al.   NATURE

Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry

(2020) Akshay Sridhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of OCT4-SOX2 motif readout on nucleosomes

(2020) Alicia K. Michael et al.   SCIENCE

The Set1 N-terminal domain and Swd2 interact with RNA polymerase II CTD to recruit COMPASS

(2020) Hyun Jin Bae et al.   Nature Communications

Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

(2020) Anand Ranjan et al.   eLife

Primary Role of the Nucleosome

(2020) Roger D. Kornberg et al.   MOLECULAR CELL

Redefining fundamental concepts of transcription initiation in bacteria

(2020) Citlalli Mejía-Almonte et al.   NATURE REVIEWS GENETICS

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid–liquid phase separation

(2020) Anne-Marie Ladouceur et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

(2020) Michiel J. Thiecke et al.   Cell Reports

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

(2020) Pabitra K. Parua et al.   Nature Communications

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting

(2020) Nicholas C. Lammers et al.   CURRENT OPINION IN CELL BIOLOGY

Pre-termination Transcription Complex: Structure and Function

(2020) Zhitai Hao et al.   MOLECULAR CELL

H1 histones control the epigenetic landscape by local chromatin compaction

(2020) Michael A. Willcockson et al.   NATURE

Measuring DNA mechanics on the genome scale

(2020) Aakash Basu et al.   NATURE

Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture

(2020) Nevin Yusufova et al.   NATURE

Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ

(2020) Nelly Said et al.   SCIENCE

Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging

(2020) Hugo B. Brandão et al.   CURRENT OPINION IN CELL BIOLOGY

Determining the effects of DNA sequence on Hel308 helicase translocation along single-stranded DNA using nanopore tweezers

(2019) Jonathan M Craig et al.   NUCLEIC ACIDS RESEARCH

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

Gene-Specific H1 Eviction through a Transcriptional Activator→p300→NAP1→H1 Pathway

(2019) Miho Shimada et al.   MOLECULAR CELL

Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

(2019) Andrés M. Cardozo Gizzi et al.   MOLECULAR CELL

R-Loops as Cellular Regulators and Genomic Threats

(2019) Madzia P. Crossley et al.   MOLECULAR CELL

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Mechanisms of σ54-Dependent Transcription Initiation and Regulation

(2019) Amy E. Danson et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation

(2019) Mo’men Abdelkareem et al.   MOLECULAR CELL

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Mechanisms of Transcriptional Pausing in Bacteria

(2019) Jin Young Kang et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Features of Transcription Factors Associating with Nucleosome Binding

(2019) Meilin Fernandez Garcia et al.   MOLECULAR CELL

Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions

(2019) Rajarshi P. Ghosh et al.   Nature Communications

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation

(2019) Malgorzata Krajewska et al.   Nature Communications

Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications

(2019) Célia Jeronimo et al.   Cell Reports

High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier

(2019) Zhijie Chen et al.   eLife

Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling

(2019) Sangjin Kim et al.   CELL

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

(2019) Alicia V. Zamudio et al.   MOLECULAR CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

Structural basis of nucleosome recognition and modification by MLL methyltransferases

(2019) Han Xue et al.   NATURE

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

RNA polymerases as moving barriers to condensin loop extrusion

(2019) Hugo B. Brandão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quiescent Cells Actively Replenish CENP-A Nucleosomes to Maintain Centromere Identity and Proliferative Potential

(2019) S. Zachary Swartz et al.   DEVELOPMENTAL CELL

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

(2019) Kristin Abramo et al.   NATURE CELL BIOLOGY

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Exon-Mediated Activation of Transcription Starts

(2019) Ana Fiszbein et al.   CELL

A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes

(2019) Joshua D. Eaton et al.   GENES & DEVELOPMENT

Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS

(2019) Peter L. Hsu et al.   MOLECULAR CELL

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism

(2019) Michael A. Cortazar et al.   MOLECULAR CELL

Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

(2018) Virginia S. Lioy et al.   CELL

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling

(2018) Justin Brumbaugh et al.   CELL

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

The cryo-EM resolution revolution and transcription complexes

(2018) Jonas Hanske et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

(2018) Joshua D. Eaton et al.   GENES & DEVELOPMENT

Centromere transcription allows CENP-A to transit from chromatin association to stable incorporation

(2018) Georg O.M. Bobkov et al.   JOURNAL OF CELL BIOLOGY

Quantitative imaging of chromatin decompaction in living cells

(2018) Elisa Dultz et al.   MOLECULAR BIOLOGY OF THE CELL

RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing

(2018) Jin Young Kang et al.   MOLECULAR CELL

Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription

(2018) Slawomir Kubik et al.   MOLECULAR CELL

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation

(2018) Robert Glyde et al.   MOLECULAR CELL

Structural Basis for NusA Stabilized Transcriptional Pausing

(2018) Xieyang Guo et al.   MOLECULAR CELL

StpA and Hha stimulate pausing by RNA polymerase by promoting DNA–DNA bridging of H-NS filaments

(2018) Beth A Boudreau et al.   NUCLEIC ACIDS RESEARCH

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast

(2018) Gregory T. Booth et al.   Nature Communications

A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication

(2018) Monica S. Guo et al.   CELL

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin

(2018) Shujun Cai et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

Transcription-associated histone pruning demarcates macroH2A chromatin domains

(2018) Zhen Sun 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

Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5′ Pause Release, Termination, and Transcription Elongation Rate

(2018) Ryan M. Sheridan 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

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Structure of human TFIID and mechanism of TBP loading onto promoter DNA

(2018) Avinash B. Patel et al.   SCIENCE

Structure of transcribing RNA polymerase II-nucleosome complex

(2018) Lucas Farnung et al.   Nature Communications

Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination

(2018) Tea Kecman et al.   Cell Reports

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

(2017) Sergey Alekseev et al.   MOLECULAR CELL

SAGA Is a General Cofactor for RNA Polymerase II Transcription

(2017) Tiago Baptista et al.   MOLECULAR CELL

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation

(2017) Robert Glyde 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

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

(2017) Nian Liu et al.   NATURE

Structures of transcription pre-initiation complex with TFIIH and Mediator

(2017) S. Schilbach et al.   NATURE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

(2017) Georg A. Busslinger et al.   NATURE

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

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

Understanding nucleosome dynamics and their links to gene expression and DNA replication

(2017) William K. M. Lai et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

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

Emerging roles of linker histones in regulating chromatin structure and function

(2017) Dmitry V. Fyodorov et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome

(2017) John B. Crickard et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure ofAquifex aeolicusσNbound to promoter DNA and the structure of σN-holoenzyme

(2017) Elizabeth A. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

The mechanism of variability in transcription start site selection

(2017) Libing Yu et al.   eLife

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

(2017) Hamish W King et al.   eLife

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Shhand ZRS enhancer colocalisation is specific to the zone of polarising activity

(2016) Iain Williamson et al.   DEVELOPMENT

Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries

(2016) Tung BK Le et al.   EMBO JOURNAL

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

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

The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6

(2016) S. Branden Van Oss et al.   MOLECULAR CELL

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

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

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

(2016) Viviana I. Risca et al.   NATURE

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mapping the 3D genome: Aiming for consilience

(2016) Job Dekker   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Roles of eukaryotic topoisomerases in transcription, replication and genomic stability

(2016) Yves Pommier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Cryo-Electron Tomography: Can it Reveal the Molecular Sociology of Cells in Atomic Detail?

(2016) Martin Beck et al.   TRENDS IN CELL BIOLOGY

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

Transcription Termination: Variations on Common Themes

(2016) Odil Porrua et al.   TRENDS IN GENETICS

H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation

(2016) Jinzen Ikebe et al.   PLoS Computational Biology

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

(2015) Ram Madabhushi et al.   CELL

The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations

(2015) Célia Jeronimo et al.   MOLECULAR CELL

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

(2015) Yuhong Zuo et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

RNA-mediated epigenetic regulation of gene expression

(2015) Daniel Holoch et al.   NATURE REVIEWS GENETICS

Getting up to speed with transcription elongation by RNA polymerase II

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

CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition

(2015) Brian Bae et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation

(2015) James Fishburn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

(2015) S. J. Philips et al.   SCIENCE

Mechanism of Transcriptional Bursting in Bacteria

(2014) Shasha Chong et al.   CELL

A Tale of Chromatin and Transcription in 100 Structures

(2014) Patrick Cramer   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Post-Translational Modifications of Histones That Influence Nucleosome Dynamics

(2014) Gregory D. Bowman et al.   CHEMICAL REVIEWS

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

(2014) B. Lackford et al.   EMBO JOURNAL

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

(2014) Aydan Bulut-Karslioglu et al.   MOLECULAR CELL

A promoter-level mammalian expression atlas

(2014)   NATURE

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   SCIENCE

Interactions between RNA polymerase and the "core recognition element" counteract pausing

(2014) I. O. Vvedenskaya et al.   SCIENCE

Control of Transcriptional Elongation

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

LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation

(2013) Irina Solovei et al.   CELL

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

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states

(2013) F. Pontvianne et al.   GENES & DEVELOPMENT

Topoisomerases facilitate transcription of long genes linked to autism

(2013) Ian F. King et al.   NATURE

Structural visualization of key steps in human transcription initiation

(2013) Yuan He et al.   NATURE

A unique Oct4 interface is crucial for reprogramming to pluripotency

(2013) Daniel Esch et al.   NATURE CELL BIOLOGY

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-generated torsional stress destabilizes nucleosomes

(2013) Sheila S Teves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-dependent dynamic supercoiling is a short-range genomic force

(2013) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti 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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2012) Elphège P. Nora et al.   NATURE

Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast

(2012) A. S. Piro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rates of Gyrase Supercoiling and Transcription Elongation Control Supercoil Density in a Bacterial Chromosome

(2012) Nikolay Rovinskiy et al.   PLoS Genetics

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

(2011) Andrey Feklistov et al.   CELL

Establishment and Maintenance of Alternative Chromatin States at a Multicopy Gene Locus

(2011) Manuel Wittner et al.   CELL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Bacterial Transcription Terminators: The RNA 3′-End Chronicles

(2011) Jason M. Peters et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis of RNA polymerase II backtracking, arrest and reactivation

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

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

All tangled up: how cells direct, manage and exploit topoisomerase function

(2011) Seychelle M. Vos et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12

(2011) Ana I. Prieto et al.   NUCLEIC ACIDS RESEARCH

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

(2011) Elizabeth A. Rach et al.   PLoS Genetics

An allosteric mechanism of Rho-dependent transcription termination

(2010) Vitaly Epshtein et al.   NATURE

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

(2010) Shane C. Dillon et al.   NATURE REVIEWS MICROBIOLOGY

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RAD6-Mediated Transcription-Coupled H2B Ubiquitylation Directly Stimulates H3K4 Methylation in Human Cells

(2009) Jaehoon Kim et al.   CELL

Regulator Trafficking on Bacterial Transcription Units In Vivo

(2009) Rachel A. Mooney et al.   MOLECULAR CELL

Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

(2009) Z. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

The RNA polymerase II core promoter — the gateway to transcription

(2008) Tamar Juven-Gershon et al.   CURRENT OPINION IN CELL BIOLOGY

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

(2008) D. A. Hendrix et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA