The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model

Heat shock induces premature transcript termination and reconfigures the human transcriptome

(2022) Simona Cugusi et al.   MOLECULAR CELL

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

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

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

(2021) Stephin J. Vervoort et al.   CELL

Conserved DNA sequence features underlie pervasive RNA polymerase pausing

(2021) Martyna Gajos et al.   NUCLEIC ACIDS RESEARCH

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

(2021) Shibin Hu et al.   MOLECULAR CELL

STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts

(2021) Joshua T. Zimmer et al.   MOLECULAR CELL

Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination

(2021) Ashwin Narain et al.   MOLECULAR CELL

SPT5 stabilization of promoter-proximal RNA polymerase II

(2021) Yuki Aoi et al.   MOLECULAR CELL

Structural basis of Integrator-mediated transcription regulation

(2021) Isaac Fianu et al.   SCIENCE

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

(2020) Yuki Aoi et al.   MOLECULAR CELL

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

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

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

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

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

(2020) Behnam Nabet 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

Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription

(2020) Grace A. Rosen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DEBrowser: interactive differential expression analysis and visualization tool for count data

(2019) Alper Kucukural et al.   BMC GENOMICS

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

(2019) Apoorva Baluapuri et al.   MOLECULAR CELL

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

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

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

Dynamic turnover of paused Pol II complexes at human promoters

(2018) Benjamin Erickson et al.   GENES & DEVELOPMENT

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

(2018) Pabitra K. Parua et al.   NATURE

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

Structure and nucleic acid binding properties of KOW domains 4 and 6–7 of human transcription elongation factor DSIF

(2018) Philipp K. Zuber et al.   Scientific Reports

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

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

(2017) Tom Smith et al.   GENOME RESEARCH

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

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

Application of a Schizosaccharomyces pombe Edc1-fused Dcp1–Dcp2 decapping enzyme for transcription start site mapping

(2017) David R. Paquette et al.   RNA

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

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

Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins

(2016) Ryan M. Sheridan et al.   BIOTECHNIQUES

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

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

(2015) Takayuki Nojima et al.   CELL

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers 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

Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways

(2015) Xiuli Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

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

(2014) Marco Saponaro et al.   CELL

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

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

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Interactions between RNA polymerase and the "core recognition element" counteract pausing

(2014) I. O. Vvedenskaya et al.   SCIENCE

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

(2014) Iris Jonkers et al.   eLife

NusG-Spt5 Proteins—Universal Tools for Transcription Modification and Communication

(2013) Sushil Kumar Tomar et al.   CHEMICAL REVIEWS

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination

(2013) P. A. Ginno et al.   GENOME RESEARCH

Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin

(2013) A. D. Wier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

(2012) B. Zamft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

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

Repression of RNA Polymerase II Elongation In Vivo Is Critically Dependent on the C-Terminus of Spt5

(2009) Hui Chen et al.   PLoS One