Eukaryotic core promoters and the functional basis of transcription initiation

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

(2018) Matthias Muhar et al.   SCIENCE

The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters

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

Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction

(2017) Britta Mueller et al.   GENES & DEVELOPMENT

Identification of Regions in the Spt5 Subunit of DRB Sensitivity-inducing Factor (DSIF) That Are Involved in Promoter-proximal Pausing

(2017) Yijun Qiu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SAGA Is a General Cofactor for RNA Polymerase II Transcription

(2017) Tiago Baptista et al.   MOLECULAR CELL

CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II

(2017) Ann Boija et al.   MOLECULAR CELL

Correlation Does Not Imply Causation: Histone Methyltransferases, but Not Histone Methylation, SET the Stage for Enhancer Activation

(2017) Tim Pollex 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

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment

(2017) Georg E. Winter 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

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

A heterochromatin-dependent transcription machinery drives piRNA expression

(2017) Peter Refsing Andersen et al.   NATURE

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Promoter shape varies across populations and affects promoter evolution and expression noise

(2017) Ignacio E Schor et al.   NATURE GENETICS

Promoting transcription over long distances

(2017) Rui R Catarino et al.   NATURE GENETICS

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

Resolving systematic errors in widely used enhancer activity assays in human cells

(2017) Felix Muerdter et al.   NATURE METHODS

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

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

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

(2017) Haruhiko Ehara et al.   SCIENCE

PAF1 regulation of promoter-proximal pause release via enhancer activation

(2017) Fei Xavier Chen et al.   SCIENCE

Blocking promiscuous activation at cryptic promoters directs cell type–specific gene expression

(2017) Jongmin Kim et al.   SCIENCE

Can We Predict Gene Expression by Understanding Proximal Promoter Architecture?

(2017) Łukasz Huminiecki et al.   TRENDS IN BIOTECHNOLOGY

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

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

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Gene Regulation: Activation through Space

(2016) Felix Muerdter et al.   CURRENT BIOLOGY

Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis

(2016) Zhengjian Zhang et al.   GENES & DEVELOPMENT

Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture

(2016) Thomas Eychenne et al.   GENES & DEVELOPMENT

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

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

High-throughput functional comparison of promoter and enhancer activities

(2016) Thomas A. Nguyen et al.   GENOME RESEARCH

EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation

(2016) Suman K. Pradhan et al.   MOLECULAR CELL

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon 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

Genome-wide mapping of autonomous promoter activity in human cells

(2016) Joris van Arensbergen et al.   NATURE BIOTECHNOLOGY

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

(2016) Cosmas D Arnold et al.   NATURE BIOTECHNOLOGY

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles

(2016) François Spitz   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors

(2016) Muhammad A. Zabidi et al.   TRENDS IN GENETICS

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

(2016) Jakub Mieczkowski et al.   Nature Communications

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

(2016) René Dreos et al.   PLoS Computational Biology

PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II

(2015) Fei Xavier Chen et al.   CELL

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Core promoter sequence in yeast is a major determinant of expression level

(2015) Shai Lubliner et al.   GENOME RESEARCH

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

Human Gene Promoters Are Intrinsically Bidirectional

(2015) Robin Andersson et al.   MOLECULAR CELL

Human Promoters Are Intrinsically Directional

(2015) Sascha H.C. Duttke et al.   MOLECULAR CELL

BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia

(2015) Jae-Seok Roe et al.   MOLECULAR CELL

Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast

(2015) Slawomir Kubik et al.   MOLECULAR CELL

Pausing of RNA Polymerase II Regulates Mammalian Developmental Potential through Control of Signaling Networks

(2015) Lucy H. Williams et al.   MOLECULAR CELL

Transcriptional plasticity promotes primary and acquired resistance to BET inhibition

(2015) Philipp Rathert et al.   NATURE

Structural basis of transcription initiation by RNA polymerase II

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

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model

(2014) Robin Andersson   BIOESSAYS

Subnucleosomal Structures and Nucleosome Asymmetry across a Genome

(2014) Ho Sung Rhee et al.   CELL

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation

(2014) Albert J. Keung et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

TRF2, but not TBP, mediates the transcription of ribosomal protein genes

(2014) Y.-L. Wang 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

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Enhancer Malfunction in Cancer

(2014) Hans-Martin Herz et al.   MOLECULAR CELL

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

(2014) Christopher M. Weber et al.   MOLECULAR CELL

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   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

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Histone core modifications regulating nucleosome structure and dynamics

(2014) Peter Tessarz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

In search of the determinants of enhancer–promoter interaction specificity

(2014) Joris van Arensbergen et al.   TRENDS IN CELL BIOLOGY

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

Divergent transcription is associated with promoters of transcriptional regulators

(2013) Cyrille Lepoivre et al.   BMC GENOMICS

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

(2013) Andreas H. Ehrensberger et al.   CELL

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Regulation of Transcription through Acetylation of H3K122 on the Lateral Surface of the Histone Octamer

(2013) Philipp Tropberger et al.   CELL

Transitions for Regulating Early Transcription

(2013) Margaux Michel et al.   CELL

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

(2013) Mounia Lagha et al.   CELL

Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

(2013) Jian Li et al.   EMBO JOURNAL

The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures

(2013) R. A.- J. Chen et al.   GENOME RESEARCH

Acetylation of RNA Polymerase II Regulates Growth-Factor-Induced Gene Transcription in Mammalian Cells

(2013) Sebastian Schröder et al.   MOLECULAR CELL

Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals

(2013) Telmo Henriques et al.   MOLECULAR CELL

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova 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

A Histone Mutant Reproduces the Phenotype Caused by Loss of Histone-Modifying Factor Polycomb

(2013) A. R. Pengelly et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

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

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

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies

(2012) Tina W. Han et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Transcription in the Absence of Histone H3.2 and H3K4 Methylation

(2012) Martina Hödl et al.   CURRENT BIOLOGY

Noise-mean relationship in mutated promoters

(2012) G. Hornung et al.   GENOME RESEARCH

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

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

(2012) Ho Sung Rhee et al.   NATURE

Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

(2012) Stefan Bonn et al.   Nature Protocols

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc

(2011) Jake E. Delmore et al.   CELL

Pioneer transcription factors: establishing competence for gene expression

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

RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia

(2011) Johannes Zuber et al.   NATURE

Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation

(2011) Rui Zhao et al.   NATURE CELL BIOLOGY

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perspectives on the RNA polymerase II core promoter

(2011) James T. Kadonaga   Wiley Interdisciplinary Reviews-Developmental Biology

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes

(2010) Ricky S Joshi et al.   EMBO JOURNAL

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

(2010) T. J. Parry et al.   GENES & DEVELOPMENT

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation

(2010) Gabor Papai et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation

(2010) James A. Goodrich et al.   NATURE REVIEWS GENETICS

Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex

(2010) A. Missra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Transcription in the Absence of Histone H3.3

(2009) Martina Hödl et al.   CURRENT BIOLOGY

Structures of three distinct activator-TFIID complexes

(2009) W.-L. Liu et al.   GENES & DEVELOPMENT

A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histones Defines the Effects of H3 K56 Acetylation

(2009) Heinz Neumann et al.   MOLECULAR CELL

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses

(2009) Helge G. Roider et al.   NUCLEIC ACIDS RESEARCH

Characterization of Transcription from TATA-Less Promoters: Identification of a New Core Promoter Element XCPE2 and Analysis of Factor Requirements

(2009) Ramakrishnan Anish et al.   PLoS One

Synchronous and Stochastic Patterns of Gene Activation in theDrosophilaEmbryo

(2009) Alistair N. Boettiger et al.   SCIENCE

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne 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

Transcriptional features of genomic regulatory blocks

(2009) Altuna Akalin et al.   GENOME BIOLOGY

Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3

(2008) Vivek Sarojkumar Chopra et al.   DEVELOPMENTAL BIOLOGY

Caudal, a key developmental regulator, is a DPE-specific transcriptional factor

(2008) T. Juven-Gershon et al.   GENES & DEVELOPMENT

Mediator-Dependent Recruitment of TFIIH Modules in Preinitiation Complex

(2008) Cyril Esnault et al.   MOLECULAR CELL

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich 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

Tools for neuroanatomy and neurogenetics in Drosophila

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

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE