RNA polymerase II pausing as a context-dependent reader of the genome

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

(2015) Fei Chen et al.   GENES & DEVELOPMENT

Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing

(2015) Diana A. Stavreva et al.   GENOME RESEARCH

Neuronal identity genes regulated by super-enhancers are preferentially down-regulated in the striatum of Huntington's disease mice

(2015) M. Achour et al.   HUMAN MOLECULAR GENETICS

Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide

(2015) Adrian T. Grzybowski 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

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

Histone exchange, chromatin structure and the regulation of transcription

(2015) Swaminathan Venkatesh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Getting up to speed with transcription elongation by RNA polymerase II

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

Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq

(2015) Bin Hu et al.   NUCLEIC ACIDS RESEARCH

Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells

(2015) Y. Chu et al.   NUCLEIC ACIDS RESEARCH

A positioned +1 nucleosome enhances promoter-proximal pausing

(2015) Silvia Jimeno-González et al.   NUCLEIC ACIDS RESEARCH

ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites

(2015) Claudia Carissimi et al.   NUCLEIC ACIDS RESEARCH

RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition

(2015) Ann Samarakkody et al.   NUCLEIC ACIDS RESEARCH

Transcriptional refractoriness is dependent on core promoter architecture

(2015) François Cesbron et al.   Nature Communications

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters

(2015) Nicholas J. Fuda et al.   PLoS Genetics

Compensatory induction of MYC expression by sustained CDK9 inhibition via a BRD4-dependent mechanism

(2015) Huasong Lu et al.   eLife

A simple method for generating high-resolution maps of genome-wide protein binding

(2015) Peter J Skene et al.   eLife

JARID1B Is a Luminal Lineage-Driving Oncogene in Breast Cancer

(2014) Shoji Yamamoto et al.   CANCER CELL

Argonaute-Bound Small RNAs from Promoter-Proximal RNA Polymerase II

(2014) Jesse R. Zamudio et al.   CELL

Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation

(2014) M. S. Buckley et al.   GENES & DEVELOPMENT

Regulation of RNA Polymerase II Termination by Phosphorylation of Gdown1

(2014) Jiannan Guo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrator Regulates Transcriptional Initiation and Pause Release following Activation

(2014) Alessandro Gardini et al.   MOLECULAR CELL

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

(2014) Myong-Hee Sung et al.   MOLECULAR CELL

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

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

(2014) Leighton J Core et al.   NATURE GENETICS

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release

(2014) Heeyoun Bunch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

(2014) J. P. Bothma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes

(2014) Bernd Stadelmayer et al.   Nature Communications

DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes

(2014) Junichi Yamamoto et al.   Nature Communications

Negative Elongation Factor Controls Energy Homeostasis in Cardiomyocytes

(2014) Haihui Pan et al.   Cell Reports

Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions

(2014) John M. Pagano et al.   PLoS Genetics

Brd4 and HEXIM1: Multiple Roles in P-TEFb Regulation and Cancer

(2014) Ruichuan Chen et al.   Biomed Research International

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

(2014) Peter J Skene et al.   eLife

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

(2014) Iris Jonkers et al.   eLife

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

(2013) Mounia Lagha et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

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

Negative Elongation Factor (NELF) Coordinates RNA Polymerase II Pausing, Premature Termination, and Chromatin Remodeling to Regulate HIV Transcription

(2013) Malini Natarajan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing

(2013) Jian Li et al.   MOLECULAR CELL

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

(2013) Charles G. Danko 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

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes

(2013) Nathan D. VanderKraats et al.   NUCLEIC ACIDS RESEARCH

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

(2013) H. Kwak et al.   SCIENCE

Genome-Wide Control of RNA Polymerase II Activity by Cohesin

(2013) Cheri A. Schaaf et al.   PLoS Genetics

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

(2013) Kai Chen et al.   eLife

Modeling precision treatment of breast cancer

(2013) Anneleen Daemen et al.   GENOME BIOLOGY

Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription

(2012) Martin Heidemann et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Microprocessor, Setx, Xrn2, and Rrp6 Co-operate to Induce Premature Termination of Transcription by RNAPII

(2012) Alexandre Wagschal et al.   CELL

Asymmetrically Modified Nucleosomes

(2012) Philipp Voigt et al.   CELL

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

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

(2012) Guoliang Li et al.   CELL

The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation

(2012) Chengqi Lin et al.   CELL

FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2

(2012) J. C. Schwartz et al.   GENES & DEVELOPMENT

Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks

(2012) D. A. Gilchrist et al.   GENES & DEVELOPMENT

Broad Ranges of Affinity and Specificity of Anti-Histone Antibodies Revealed by a Quantitative Peptide Immunoprecipitation Assay

(2012) Shingo Nishikori et al.   JOURNAL OF MOLECULAR BIOLOGY

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

Transcriptional Regulation by Pol II(G) Involving Mediator and Competitive Interactions of Gdown1 and TFIIF with Pol II

(2012) Miki Jishage et al.   MOLECULAR CELL

Functional Association of Gdown1 with RNA Polymerase II Poised on Human Genes

(2012) Bo Cheng 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

The Drosophila 7SK snRNP and the essential role of dHEXIM in development

(2012) Duy Nguyen et al.   NUCLEIC ACIDS RESEARCH

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

(2012) B. Zamft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complex effects of flavopiridol on the expression of primary response genes

(2012) Havva Keskin et al.   Cell Division

Serine-7 but not serine-5 phosphorylation primes RNA polymerase II CTD for P-TEFb recognition

(2012) Nadine Czudnochowski et al.   Nature Communications

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Nonspecific Transcription-Factor-DNA Binding Influences Nucleosome Occupancy in Yeast

(2011) Ariel Afek et al.   BIOPHYSICAL JOURNAL

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

Promoter-proximal Pol II: When stalling speeds things up

(2011) Sergei Nechaev et al.   CELL CYCLE

Cohesin Selectively Binds and Regulates Genes with Paused RNA Polymerase

(2011) Avery Fay et al.   CURRENT BIOLOGY

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC)

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

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

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

Genetic and Genomic Analyses of RNA Polymerase II-pausing Factor in Regulation of Mammalian Transcription and Cell Growth

(2011) Jianlong Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Negative Elongation Factor Accelerates the Rate at Which Heat Shock Genes Are Shut off by Facilitating Dissociation of Heat Shock Factor

(2011) S. K. B. Ghosh et al.   MOLECULAR AND CELLULAR BIOLOGY

H3K4 Trimethylation by Set1 Promotes Efficient Termination by the Nrd1-Nab3-Sen1 Pathway

(2011) N. Terzi et al.   MOLECULAR AND CELLULAR BIOLOGY

Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II

(2011) Ramendra N Saha et al.   NATURE NEUROSCIENCE

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

(2011) Eivind Valen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

(2011) Pascal Preker et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Bursting from the HIV-1 Promoter Is a Significant Source of Stochastic Noise in HIV-1 Gene Expression

(2010) Abhyudai Singh et al.   BIOPHYSICAL JOURNAL

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

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

(2010) Daniel A. Gilchrist et al.   CELL

Cyclin T1 overexpression induces malignant transformation and tumor growth

(2010) Cristian Moiola et al.   CELL CYCLE

CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1

(2010) B. Bartkowiak et al.   GENES & DEVELOPMENT

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

Splicing-Dependent RNA Polymerase Pausing in Yeast

(2010) Ross D. Alexander et al.   MOLECULAR CELL

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

CDK8 is a positive regulator of transcriptional elongation within the serum response network

(2010) Aaron J Donner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Activator-Mediator binding regulates Mediator-cofactor interactions

(2010) C. C. Ebmeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II

(2009) Seong Hoon Ahn et al.   EMBO JOURNAL

DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation

(2009) Y. Chen et al.   GENES & DEVELOPMENT

Human Negative Elongation Factor Activates Transcription and Regulates Alternative Transcription Initiation

(2009) Jianlong Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chromatin Structure Is Implicated in "Late" Elongation Checkpoints on the U2 snRNA and  -Actin Genes

(2009) S. Egloff et al.   MOLECULAR AND CELLULAR BIOLOGY

Triptolide is an inhibitor of RNA polymerase I and II-dependent transcription leading predominantly to down-regulation of short-lived mRNA

(2009) S. Vispe et al.   MOLECULAR CANCER THERAPEUTICS

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

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

(2009)   NATURE

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

Mouse Cofactor of BRCA1 (Cobra1) Is Required for Early Embryogenesis

(2009) Asma Amleh et al.   PLoS One

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

(2009) S. Nechaev et al.   SCIENCE

Single-Molecule Studies of RNA Polymerase: Motoring Along

(2008) Kristina M. Herbert et al.   Annual Review of Biochemistry

All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

(2008) Julian M Rozenberg et al.   BMC GENOMICS

Heterogeneity of Embryonic and Adult Stem Cells

(2008) Thomas Graf et al.   Cell Stem Cell

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

(2008) D. A. Gilchrist et al.   GENES & DEVELOPMENT

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

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

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

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

Bivalent domains enforce transcriptional memory of DNA methylated genes in cancer cells

(2008) J. Rodriguez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2008) Leighton J. Core et al.   SCIENCE

Deregulation of cofactor of BRCA1 expression in breast cancer cells

(2007) Jianlong Sun et al.   JOURNAL OF CELLULAR BIOCHEMISTRY