A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3′-processing and termination

Acute perturbation strategies in interrogating RNA polymerase II elongation factor function in gene expression

(2021) Bin Zheng et al.   GENES & DEVELOPMENT

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

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

Acute BAF perturbation causes immediate changes in chromatin accessibility

(2021) Sandra Schick et al.   NATURE GENETICS

SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation

(2021) Jingting Li et al.   Nature Communications

Conserved DNA sequence features underlie pervasive RNA polymerase pausing

(2021) Martyna Gajos et al.   NUCLEIC ACIDS RESEARCH

Using TTchem-seq for profiling nascent transcription and measuring transcript elongation

(2020) Lea H. Gregersen et al.   Nature Protocols

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

(2020) Johanna Fitz et al.   NATURE GENETICS

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

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

Termination of Transcription by RNA Polymerase II: BOOM!

(2020) Joshua D. Eaton et al.   TRENDS IN GENETICS

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

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

(2019) Apoorva Baluapuri et al.   MOLECULAR CELL

Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination

(2019) Kinga Kamieniarz-Gdula et al.   MOLECULAR CELL

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae

(2019) Mitchell A. Ellison et al.   GENETICS

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

Nascent RNA analyses: tracking transcription and its regulation

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

The Bromodomain Protein 4 Contributes to the Regulation of Alternative Splicing

(2019) Sheetal Uppal et al.   Cell Reports

Mechanistic insights into mRNA 3′-end processing

(2019) Ananthanarayanan Kumar et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes

(2019) Joshua D. Eaton et al.   GENES & DEVELOPMENT

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler 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

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

(2018) Joshua D. Eaton 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

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens

(2018) Jean-Paul Concordet et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Matthias Muhar et al.   SCIENCE

BRD4 Promotes DNA Repair and Mediates the Formation of TMPRSS2-ERG Gene Rearrangements in Prostate Cancer

(2018) Xiangyi Li et al.   Cell Reports

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

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima et al.   MOLECULAR CELL

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Carlo Baejen 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

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

(2017) Georg E. Winter et al.   MOLECULAR CELL

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

(2017) Sarah C. Hsu et al.   MOLECULAR CELL

Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation

(2017) Ka Lung Cheung et al.   MOLECULAR CELL

PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes

(2017) Ruijia Wang et al.   NUCLEIC ACIDS RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

PAF1 regulation of promoter-proximal pause release via enhancer activation

(2017) Fei Xavier Chen et al.   SCIENCE

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

(2016) Miriam Sansó et al.   GENES & DEVELOPMENT

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

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

Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

(2016) Hisham Mohammed et al.   Nature Protocols

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Structural Mechanism of Transcriptional Regulator NSD3 Recognition by the ET Domain of BRD4

(2016) Qiang Zhang et al.   STRUCTURE

PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation

(2016) Yan Yang et al.   PLoS Genetics

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

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

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

(2015) Nova Fong et al.   MOLECULAR CELL

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

(2015) Tetsushi Sakuma et al.   Nature Protocols

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes

(2015) Clélia Laitem et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary 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

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes

(2015) Clélia Laitem et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

BRD4: A BET(ter) target for the treatment of AML?

(2014) Peter Valent et al.   CELL CYCLE

3' end formation of pre-mRNA and phosphorylation of Ser2 on the RNA polymerase II CTD are reciprocally coupled in human cells

(2014) L. Davidson et al.   GENES & DEVELOPMENT

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3′ processing

(2014) Serena L. Chan et al.   GENES & DEVELOPMENT

The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition

(2014) Junwei Shi et al.   MOLECULAR CELL

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez 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

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure

(2013) Priti Anand et al.   CELL

Splicing-coupled 3′ end formation requires a terminal splice acceptor site, but not intron excision

(2013) Lee Davidson et al.   NUCLEIC ACIDS RESEARCH

RNA Polymerase II Elongation Control

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

The Spt5 C-Terminal Region Recruits Yeast 3' RNA Cleavage Factor I

(2012) A. Mayer et al.   MOLECULAR AND CELLULAR 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Two-pronged Binding with Bromodomain-containing Protein 4 Liberates Positive Transcription Elongation Factor b from Inactive Ribonucleoprotein Complexes

(2011) Sebastian Schröder et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Brd4 Extraterminal Domain Confers Transcription Activation Independent of pTEFb by Recruiting Multiple Proteins, Including NSD3

(2011) S. Rahman et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcriptional Activators Enhance Polyadenylation of mRNA Precursors

(2011) Takashi Nagaike et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Human PAF1 Complex Acts in Chromatin Transcription Elongation Both Independently and Cooperatively with SII/TFIIS

(2010) Jaehoon Kim et al.   CELL

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Transcription termination by nuclear RNA polymerases

(2009) P. Richard et al.   GENES & DEVELOPMENT

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

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

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3′ mRNA processing factors

(2009) Orit Rozenblatt-Rosen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Interactions between the Paf1 Complex and a Cleavage and Polyadenylation Factor Are Revealed by Dissociation of Paf1 from RNA Polymerase II

(2008) Kristen Nordick et al.   EUKARYOTIC CELL

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY