SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape

Integrator is a genome-wide attenuator of non-productive transcription

(2021) Søren Lykke-Andersen et al.   MOLECULAR CELL

Collaboration through chromatin: motors of transcription and chromatin structure

(2021) Nathan Gamarra et al.   JOURNAL OF MOLECULAR BIOLOGY

Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans

(2021) Roberta Dollinger et al.   JOURNAL OF MOLECULAR BIOLOGY

Fast-acting chemical tools to delineate causality in transcriptional control

(2021) Martin G. Jaeger et al.   MOLECULAR CELL

Acute BAF perturbation causes immediate changes in chromatin accessibility

(2021) Sandra Schick et al.   NATURE GENETICS

The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer

(2021) Stephin J. Vervoort et al.   CELL

Structural basis of nucleosome transcription mediated by Chd1 and FACT

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

Structural insights into preinitiation complex assembly on core promoters

(2021) Xizi Chen et al.   SCIENCE

Structure of nucleosome-bound human BAF complex

(2020) Shuang He et al.   SCIENCE

Evaluating Enhancer Function and Transcription

(2020) Andrew Field et al.   Annual Review of Biochemistry

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

Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction

(2020) Johanna Fitz et al.   NATURE GENETICS

The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

(2020) Felipe Beckedorff et al.   Cell Reports

Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription

(2020) Jenna K. Rimel et al.   GENES & DEVELOPMENT

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

Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase

(2020) Hai Zheng et al.   SCIENCE

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

The Integrator complex cleaves nascent mRNAs to attenuate transcription

(2019) Deirdre C. Tatomer et al.   GENES & DEVELOPMENT

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms

(2019) Robert G. Roeder   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2019) Nathan D. Elrod 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

Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation

(2018) Johanna Fitz et al.   EMBO JOURNAL

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

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

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Cdk9–PP1 switch regulates the elongation–termination transition of RNA polymerase II

(2018) Pabitra K. Parua et al.   NATURE

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

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

(2018) Tea Kecman et al.   Cell Reports

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

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

(2017) Carlo Baejen et al.   MOLECULAR CELL

Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation

(2017) Ameet Shetty et al.   MOLECULAR CELL

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

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

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

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

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

PAF1 regulation of promoter-proximal pause release via enhancer activation

(2017) Fei Xavier Chen et al.   SCIENCE

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

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

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

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

(2015) Fei Chen et al.   GENES & DEVELOPMENT

MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems

(2015) Tetsushi Sakuma et al.   Nature Protocols

Getting up to speed with transcription elongation by RNA polymerase II

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

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Integrator Regulates Transcriptional Initiation and Pause Release following Activation

(2014) Alessandro Gardini et al.   MOLECULAR CELL

Insights into how Spt5 functions in transcription elongation and repressing transcription coupled DNA repair

(2014) Wentao Li et al.   NUCLEIC ACIDS RESEARCH

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

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

(2014) Iris Jonkers et al.   eLife

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

(2013) Warren A. Whyte et al.   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

The Spt4–Spt5 complex: A multi-faceted regulator of transcription elongation

(2012) Grant A. Hartzog et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

Cross-talk Among RNA Polymerase II Kinases Modulates C-terminal Domain Phosphorylation

(2012) Ballachanda N. Devaiah et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Role of human transcription elongation factor DSIF in the suppression of senescence and apoptosis

(2009) Toshiharu Komori et al.   GENES TO CELLS

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY