Control of non-productive RNA polymerase II transcription via its early termination in metazoans

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

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

Structure of a transcribing RNA polymerase II–U1 snRNP complex

(2021) Suyang Zhang et al.   SCIENCE

Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans

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

Structure of the catalytic core of the Integrator complex

(2021) Moritz M. Pfleiderer et al.   MOLECULAR CELL

Efficient RNA polymerase II pause release requires U2 snRNP function

(2021) Livia Caizzi 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

Protein phosphatases in the RNAPII transcription cycle: erasers, sculptors, gatekeepers, and potential drug targets

(2021) Giacomo Cossa et al.   GENES & DEVELOPMENT

A first exon termination checkpoint preferentially suppresses extragenic transcription

(2021) Liv M. I. Austenaa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ZC3H4 restricts non-coding transcription in human cells

(2021) Chris Estell et al.   eLife

ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control

(2021) Søren Lykke-Andersen et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

RNA polymerase II speed: a key player in controlling and adapting transcriptome composition

(2021) Lisa Muniz et al.   EMBO JOURNAL

Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo

(2021) Kristina Žumer et al.   MOLECULAR CELL

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

(2021) Mirjam Arnold 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

Who let the DoGs out? – biogenesis of stress-induced readthrough transcripts

(2021) Nicolle A. Rosa-Mercado et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structural basis of Integrator-mediated transcription regulation

(2021) Isaac Fianu et al.   SCIENCE

Integrator enforces the fidelity of transcriptional termination at protein-coding genes

(2021) Lucas Ferreira Dasilva et al.   Science Advances

A transcriptome-wide antitermination mechanism sustaining identity of embryonic stem cells

(2020) Yaroslav A. Kainov et al.   Nature Communications

A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome

(2020) Guifen Wu et al.   Cell Reports

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

(2020) Yuki Aoi et al.   MOLECULAR CELL

CDK11 is required for transcription of replication-dependent histone genes

(2020) Pavla Gajdušková et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

(2020) Mateusz Bajczyk et al.   NUCLEIC ACIDS RESEARCH

Roles of CDK/Cyclin complexes in transcription and pre-mRNA splicing: Cyclins L and CDK11 at the cross-roads of cell cycle and regulation of gene expression

(2020) Pascal Loyer et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

CDK13 cooperates with CDK12 to control global RNA polymerase II processivity

(2020) Zheng Fan et al.   Science Advances

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

(2020) Michael Tellier et al.   NUCLEIC ACIDS RESEARCH

INTS10–INTS13–INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module

(2020) Kevin Sabath et al.   Nature Communications

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

(2020) Felipe Beckedorff et al.   Cell Reports

Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1

(2020) Jasmine Barra et al.   Science Advances

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

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

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

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

(2020) Hai Zheng et al.   SCIENCE

The multifaceted eukaryotic cap structure

(2020) Jerry Pelletier et al.   Wiley Interdisciplinary Reviews-RNA

Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes

(2019) Eva Gómez-Orte et al.   PLoS Genetics

Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes

(2019) Ruijia Wang et al.   Cell Reports

U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene Regulation

(2019) Christopher C. Venters et al.   Cold Spring Harbor Perspectives in Biology

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

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

Structural insights into the 3’-end mRNA maturation machinery: snapshot on Polyadenylation signal recognition

(2019) Stéphane Thore et al.   BIOCHIMIE

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins

(2019) Lea H. Gregersen et al.   CELL

The Integrator complex cleaves nascent mRNAs to attenuate transcription

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

A Complex of U1 snRNP with Cleavage and Polyadenylation Factors Controls Telescripting, Regulating mRNA Transcription in Human Cells

(2019) Byung Ran So et al.   MOLECULAR CELL

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

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

Transcriptional Control by Premature Termination: A Forgotten Mechanism

(2019) Kinga Kamieniarz-Gdula et al.   TRENDS IN GENETICS

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

(2019) Joshua D. Eaton 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

The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay

(2019) Toomas Silla et al.   NUCLEIC ACIDS RESEARCH

Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals

(2018) Nilay Shah et al.   MOLECULAR CELL

Targeted Enhancer Activation by a Subunit of the Integrator Complex

(2018) Elisa Barbieri et al.   MOLECULAR CELL

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

Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting

(2018) Wiebke Manuela Schulze et al.   Nature Communications

The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts

(2018) Toomas Silla et al.   Cell Reports

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

Escaping nuclear decay: the significance of mRNA export for gene expression

(2018) Agnieszka Tudek et al.   CURRENT GENETICS

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

CDK12 regulates DNA repair genes by suppressing intronic polyadenylation

(2018) Sara J. Dubbury et al.   NATURE

An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression

(2017) Koichi Ogami et al.   GENES & DEVELOPMENT

Integrator orchestrates RAS/ERK1/2 signaling transcriptional programs

(2017) Jingyin Yue et al.   GENES & DEVELOPMENT

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

ARS2 is a general suppressor of pervasive transcription

(2017) Claudia Iasillo et al.   NUCLEIC ACIDS RESEARCH

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

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate

(2017) Simone Giacometti et al.   Cell Reports

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Co-transcriptional splicing and the CTD code

(2016) Noélia Custódio et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

(2016) Tassa Saldi et al.   JOURNAL OF MOLECULAR BIOLOGY

Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts

(2016) Nicola Meola et al.   MOLECULAR CELL

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Architecture and RNA binding of the human negative elongation factor

(2016) Seychelle M Vos et al.   eLife

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

(2015) Takayuki Nojima et al.   CELL

The Integrator complex controls the termination of transcription at diverse classes of gene targets

(2015) Jeffrey R Skaar et al.   CELL RESEARCH

Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

(2015) Liv M.I. Austenaa et al.   MOLECULAR CELL

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

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

Suppressor of sable [Su(s)] and Wdr82 down-regulate RNA from heat-shock-inducible repetitive elements by a mechanism that involves transcription termination

(2015) Paul Brewer-Jensen et al.   RNA

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

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

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

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

(2014) Seung Park et al.   BMC GENOMICS

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

Integrator Regulates Transcriptional Initiation and Pause Release following Activation

(2014) Alessandro Gardini et al.   MOLECULAR CELL

Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes

(2014) Bernd Stadelmayer et al.   Nature Communications

DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes

(2014) Junichi Yamamoto et al.   Nature Communications

The structure and substrate specificity of human Cdk12/Cyclin K

(2014) Christian A. Bösken et al.   Nature Communications

RNA Polymerase II Transcription Elongation Control

(2013) Jiannan Guo et al.   CHEMICAL REVIEWS

Quantitative Dissection and Stoichiometry Determination of the Human SET1/MLL Histone Methyltransferase Complexes

(2013) R. van Nuland et al.   MOLECULAR AND CELLULAR BIOLOGY

Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals

(2013) Telmo Henriques et al.   MOLECULAR CELL

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

CBC–ARS2 stimulates 3′-end maturation of multiple RNA families and favors cap-proximal processing

(2013) Marie Hallais et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The human cap-binding complex is functionally connected to the nuclear RNA exosome

(2013) Peter Refsing Andersen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

snRNA 3' End Formation Requires Heterodimeric Association of Integrator Subunits

(2012) T. R. Albrecht et al.   MOLECULAR AND CELLULAR BIOLOGY

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II

(2012) Stéphane Larochelle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo

(2012) Bo Gu et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Transcription attenuation in bacteria: theme and variations

(2011) M. Naville et al.   Briefings in Functional Genomics

Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex

(2011) Michal Lubas et al.   MOLECULAR CELL

Ser7 Phosphorylation of the CTD Recruits the RPAP2 Ser5 Phosphatase to snRNA Genes

(2011) Sylvain Egloff et al.   MOLECULAR CELL

The Integrator Complex Recognizes a New Double Mark on the RNA Polymerase II Carboxyl-terminal Domain

(2010) Sylvain Egloff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Tandem SH2 Domain in Transcription Elongation Factor Spt6 Binds the Phosphorylated RNA Polymerase II C-terminal Repeat Domain (CTD)

(2010) Mai Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification and Characterization of a Novel Human PP1 Phosphatase Complex

(2010) Jeong-Heon Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation

(2010) Stefania Millevoi et al.   NUCLEIC ACIDS RESEARCH

Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

(2009) Melissa J. Moore et al.   CELL

Ars2 Regulates Both miRNA- and siRNA- Dependent Silencing and Suppresses RNA Virus Infection in Drosophila

(2009) Leah R. Sabin et al.   CELL

Ars2 Links the Nuclear Cap-Binding Complex to RNA Interference and Cell Proliferation

(2009) Joshua J. Gruber et al.   CELL

TFIIH-Associated Cdk7 Kinase Functions in Phosphorylation of C-Terminal Domain Ser7 Residues, Promoter-Proximal Pausing, and Termination by RNA Polymerase II

(2009) K. Glover-Cutter et al.   MOLECULAR AND CELLULAR BIOLOGY

TFIIH Kinase Places Bivalent Marks on the Carboxy-Terminal Domain of RNA Polymerase II

(2009) Md. Sohail Akhtar et al.   MOLECULAR CELL

“Cotranscriptionality”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions

(2009) Roberto Perales et al.   MOLECULAR CELL

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

(2009) Yongsheng Shi et al.   MOLECULAR CELL

Molecular Regulation of H3K4 Trimethylation by Wdr82, a Component of Human Set1/COMPASS

(2008) M. Wu et al.   MOLECULAR AND CELLULAR BIOLOGY

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

(2008) S. Laubinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA