A dual role for H2A.Z.1 in modulating the dynamics of RNA polymerase II initiation and elongation

Structural basis of nucleosome transcription mediated by Chd1 and FACT

(2021) Lucas Farnung et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation

(2020) Assala Lamaa et al.   eLife

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

(2020) Yuki Aoi et al.   MOLECULAR CELL

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

(2020) Anand Ranjan et al.   eLife

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

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

(2019) Zhijie Chen et al.   eLife

Single Amino Acid Change Underlies Distinct Roles of H2A.Z Subtypes in Human Syndrome

(2019) Rachel S. Greenberg et al.   CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

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

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

(2018) Glòria Mas et al.   NATURE GENETICS

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

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

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Global inhibition of transcription causes an increase in histone H2A.Z incorporation within gene bodies

(2017) Anahita Lashgari et al.   NUCLEIC ACIDS RESEARCH

The Histone Variant H2A.Z Is a Master Regulator of the Epithelial-Mesenchymal Transition

(2017) Renae Domaschenz et al.   Cell Reports

Cryo-EM in the study of challenging systems: the human transcription pre-initiation complex

(2016) Eva Nogales et al.   CURRENT OPINION IN STRUCTURAL 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

Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing

(2016) Andreas Mayer et al.   Nature Protocols

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

The E3 ubiquitin ligase activity of RING1B is not essential for early mouse development

(2015) Robert S. Illingworth et al.   GENES & DEVELOPMENT

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

(2015) Fei Chen et al.   GENES & DEVELOPMENT

GC skew defines distinct RNA polymerase pause sites in CpG island promoters

(2015) Wendy A. Kellner et al.   GENOME RESEARCH

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

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury 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

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data

(2014) Yanxiao Zhang et al.   BIOINFORMATICS

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

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

Every amino acid matters: essential contributions of histone variants to mammalian development and disease

(2014) Ian Maze et al.   NATURE REVIEWS GENETICS

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

(2014) Iris Jonkers et al.   eLife

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

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

(2013) H. Kwak et al.   SCIENCE

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

(2013) I. I. Cisse et al.   SCIENCE

H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation

(2013) Vidya Subramanian et al.   PLoS Genetics

Floating-Harbor syndrome and polycystic kidneys associated withSRCAPmutation

(2012) Michael Reschen et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

(2012) Gangqing Hu et al.   Cell Stem Cell

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Histone H2A.Z inheritance during the cell cycle and its impact on promoter organization and dynamics

(2012) Maxim Nekrasov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

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

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

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

H2A.Z overexpression promotes cellular proliferation of breast cancer cells

(2010) Amy Svotelis et al.   CELL CYCLE

Chromatin interaction of TATA-binding protein is dynamically regulated in human cells

(2010) P. de Graaf et al.   JOURNAL OF CELL SCIENCE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates

(2009) Deanna Dryhurst et al.   BMC BIOLOGY

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

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

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

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

(2008) Arnauld Sergé et al.   NATURE METHODS