Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo

Efficient RNA polymerase II pause release requires U2 snRNP function

(2021) Livia Caizzi et al.   MOLECULAR CELL

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

(2020) Yuki Aoi et al.   MOLECULAR CELL

Selective Mediator dependence of cell-type-specifying transcription

(2020) Martin G. Jaeger 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

CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

(2020) Michael Tellier et al.   NUCLEIC ACIDS RESEARCH

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors

(2019) Haruhiko Ehara et al.   SCIENCE

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes

(2019) Anil Paul Chirackal Manavalan et al.   EMBO REPORTS

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

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation

(2019) Malgorzata Krajewska et al.   Nature Communications

Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications

(2019) Célia Jeronimo et al.   Cell Reports

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

The Paf1 complex and P-TEFb have reciprocal and antagonist roles in maintaining multipotent neural crest progenitors

(2019) Michael J. Jurynec et al.   DEVELOPMENT

Transcription through the nucleosome

(2019) Tomoya Kujirai et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

SPT6 interacts with NSD2 and facilitates interferon-induced transcription

(2018) Ryota Ouda et al.   FEBS LETTERS

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

(2018) Anthony C. Chiu et al.   MOLECULAR CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription

(2018) David L.V. Bauer 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

The Implication of Early Chromatin Changes in X Chromosome Inactivation

(2018) Jan Jakub Żylicz et al.   CELL

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

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

Spt6 Is Required for the Fidelity of Promoter Selection

(2018) Stephen M. Doris et al.   MOLECULAR CELL

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers

(2018) Jacob M. Tome et al.   NATURE GENETICS

Structure of transcribing RNA polymerase II-nucleosome complex

(2018) Lucas Farnung et al.   Nature Communications

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins

(2017) A. Hongjun Wang et al.   MOLECULAR CELL

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

(2017) Margarita Schlackow et al.   MOLECULAR CELL

Nucleosome–Chd1 structure and implications for chromatin remodelling

(2017) Lucas Farnung et al.   NATURE

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation

(2017) S. Branden Van Oss et al.   TRENDS IN BIOCHEMICAL SCIENCES

A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription

(2017) Matthew A Sdano et al.   eLife

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes

(2016) Heeyoun Bunch et al.   GENOMICS

Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide

(2016) Takayuki Nojima et al.   Nature Protocols

Histone variants on the move: substrates for chromatin dynamics

(2016) Paul B. Talbert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum

(2016) Sophie H. Adjalley et al.   Cell Reports

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

(2016) Yan Yang et al.   PLoS Genetics

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

(2015) Takayuki Nojima et al.   CELL

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

(2015) Vicent Pelechano et al.   CELL

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

(2015) Fei Xavier Chen et al.   CELL

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

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

Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex

(2015) Qing-Fu Cao et al.   MOLECULAR AND CELLULAR BIOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

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

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

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

(2014) Marco Saponaro et al.   CELL

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

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

(2014) Christopher M. Weber 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

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   SCIENCE

Transcribing through the nucleosome

(2014) Sheila S. Teves et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2014) Iris Jonkers et al.   eLife

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

(2014) Gilad Fuchs et al.   GENOME BIOLOGY

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

(2013) Andreas H. Ehrensberger et al.   CELL

Gene promoters dictate histone occupancy within genes

(2013) Roberto Perales et al.   EMBO JOURNAL

Structural insights into Paf1 complex assembly and histone binding

(2013) Xinlei Chu et al.   NUCLEIC ACIDS RESEARCH

RNA Polymerase II Elongation Control

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

Mechanism of transcription through a nucleosome by RNA polymerase II

(2012) Olga I. Kulaeva et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Transcription elongation factors DSIF and NELF: Promoter-proximal pausing and beyond

(2012) Yuki Yamaguchi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Promoter proximal pausing and the control of gene expression

(2011) Jian Li et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The PAF1 complex differentially regulates cardiomyocyte specification

(2011) Adam D. Langenbacher et al.   DEVELOPMENTAL BIOLOGY

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

(2010) Jaehoon Kim 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

The PAF1 complex component Leo1 is essential for cardiac and neural crest development in zebrafish

(2010) Catherine T. Nguyen et al.   DEVELOPMENTAL BIOLOGY

A Genome-Scale RNAi Screen for Oct4 Modulators Defines a Role of the Paf1 Complex for Embryonic Stem Cell Identity

(2009) Li Ding et al.   Cell Stem Cell

Spt6 enhances the elongation rate of RNA polymerase II in vivo

(2009) M Behfar Ardehali et al.   EMBO JOURNAL

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

(2009) S. Nechaev et al.   SCIENCE

The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation

(2008) S. M. Yoh et al.   GENES & DEVELOPMENT

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