Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans

Stress-induced nuclear condensation of NELF drives transcriptional downregulation

(2021) Prashant Rawat et al.   MOLECULAR CELL

TFIID Enables RNA Polymerase II Promoter-Proximal Pausing

(2020) Charli B. Fant et al.   MOLECULAR CELL

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

(2020) Yuki Aoi et al.   MOLECULAR CELL

Release of promoter–proximal paused Pol II in response to histone deacetylase inhibition

(2020) Roshan Vaid et al.   NUCLEIC ACIDS RESEARCH

Epstein–Barr virus co-opts TFIIH component XPB to specifically activate essential viral lytic promoters

(2020) Dinesh Verma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The CTD Is Not Essential for the Post-Initiation Control of RNA Polymerase II Activity

(2020) Alan Gerber et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation

(2020) Seychelle M. Vos et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A unified view of the sequence and functional organization of the human RNA polymerase II promoter

(2020) Donal S Luse et al.   NUCLEIC ACIDS RESEARCH

Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)

(2020) Tim-Michael Decker   JOURNAL OF MOLECULAR BIOLOGY

Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination

(2020) Kai-Lieh Huang et al.   MOLECULAR CELL

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

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

Causes and consequences of RNA polymerase II stalling during transcript elongation

(2020) Melvin Noe Gonzalez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Multivalent Role of Human TFIID in Recruiting Elongation Components at the Promoter-Proximal Region for Transcriptional Control

(2019) Dipika Yadav et al.   Cell Reports

Promoter-proximal pausing mediated by the exon junction complex regulates splicing

(2019) Junaid Akhtar et al.   Nature Communications

Use of the nuclear walk-on methodology to determine sites of RNA polymerase II initiation and pausing and quantify nascent RNAs in cells

(2019) Christopher B. Ball et al.   METHODS

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing

(2019) Wanqing Shao et al.   eLife

Paf1C regulates RNA polymerase II progression by modulating elongation rate

(2019) Liming Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing

(2019) Theophilus T. Tettey et al.   Cell Reports

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing

(2019) Jean-Pierre Etchegaray et al.   MOLECULAR CELL

Targeting Spt5-Pol II by Small-Molecule Inhibitors Uncouples Distinct Activities and Reveals Additional Regulatory Roles

(2019) Anat Bahat et al.   MOLECULAR CELL

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

cis Elements that Mediate RNA Polymerase II Pausing Regulate Human Gene Expression

(2019) Jason A. Watts et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes

(2019) Nathan D. Elrod et al.   MOLECULAR CELL

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

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

(2018) Jin Young Kang et al.   MOLECULAR 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

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

Transient pausing by RNA polymerase II

(2018) David H. Price   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simplified ChIP-exo assays

(2018) Matthew J. Rossi et al.   Nature Communications

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

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

Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme

(2018) Tinyi Chu et al.   NATURE GENETICS

Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation

(2017) Leah A. Gates et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

(2017) Sergey Alekseev 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

Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation

(2017) Calla M Olson et al.   Nature Chemical Biology

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes

(2017) Douglas G. Baumann et al.   NUCLEIC ACIDS RESEARCH

Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome

(2017) Kyle A. Nilson et al.   NUCLEIC ACIDS RESEARCH

PAF1 regulation of promoter-proximal pause release via enhancer activation

(2017) Fei Xavier Chen et al.   SCIENCE

Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2

(2017) Wiebke Manuela Schulze et al.   Nature Communications

Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex

(2017) Jin Young Kang et al.   eLife

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Overview of CDK9 as a target in cancer research

(2016) Fatima Morales et al.   CELL CYCLE

P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates

(2016) Miriam Sansó et al.   GENES & DEVELOPMENT

Multiple P-TEFbs cooperatively regulate the release of promoter-proximally paused RNA polymerase II

(2016) Xiaodong Lu et al.   NUCLEIC ACIDS RESEARCH

GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes

(2016) Shih-Ying Tsai et al.   Epigenetics & Chromatin

Architecture and RNA binding of the human negative elongation factor

(2016) Seychelle M Vos et al.   eLife

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

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

(2015) Fei Xavier Chen et al.   CELL

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

(2015) Fei Chen et al.   GENES & DEVELOPMENT

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

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Getting up to speed with transcription elongation by RNA polymerase II

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

A positioned +1 nucleosome enhances promoter-proximal pausing

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

RNA polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II

(2015) M. Yu et al.   SCIENCE

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

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

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

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

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances

(2014) Eric D. Merkley et al.   PROTEIN SCIENCE

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

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

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

(2014) Iris Jonkers et al.   eLife

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

(2013) Jian Li et al.   EMBO JOURNAL

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

(2013) Jian Li 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

RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

The super elongation complex (SEC) family in transcriptional control

(2012) Zhuojuan Luo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman 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

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

(2010) Daniel A. Gilchrist et al.   CELL

Vertebrate Homologue of Drosophila GAGA Factor

(2010) Navneet Kaur Matharu et al.   JOURNAL OF MOLECULAR BIOLOGY

HIV-1 Tat and Host AFF4 Recruit Two Transcription Elongation Factors into a Bifunctional Complex for Coordinated Activation of HIV-1 Transcription

(2010) Nanhai He et al.   MOLECULAR CELL

AFF4, a Component of the ELL/P-TEFb Elongation Complex and a Shared Subunit of MLL Chimeras, Can Link Transcription Elongation to Leukemia

(2010) Chengqi Lin et al.   MOLECULAR CELL

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

(2010) Bijan Sobhian et al.   MOLECULAR CELL

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

Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones

(2010) R. B. Deal et al.   SCIENCE

Synchronous and Stochastic Patterns of Gene Activation in theDrosophilaEmbryo

(2009) Alistair N. Boettiger 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

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

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

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

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