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

A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription

(2014) Sebastian Marquardt et al.   CELL

Delineating the Structural Blueprint of the Pre-mRNA 3'-End Processing Machinery

(2014) K. Xiang et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition

(2014) Carlo Baejen et al.   MOLECULAR CELL

Roadblock Termination by Reb1p Restricts Cryptic and Readthrough Transcription

(2014) Jessie Colin et al.   MOLECULAR CELL

Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

(2014) Agnieszka Tudek et al.   MOLECULAR CELL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

RNA polymerase II termination involves C-terminal-domain tyrosine dephosphorylation by CPF subunit Glc7

(2014) Amelie Schreieck et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNA exosome promotes transcription termination of backtracked RNA polymerase II

(2014) Jean-François Lemay et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast

(2014) Manuele Castelnuovo et al.   NUCLEIC ACIDS RESEARCH

The Evolutionarily Conserved Pol II Flap Loop Contributes to Proper Transcription Termination on Short Yeast Genes

(2014) Erika Pearson et al.   Cell Reports

Genome-Wide Mapping of Yeast RNA Polymerase II Termination

(2014) Paul Schaughency et al.   PLoS Genetics

A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs

(2013) Alex Charles Tuck et al.   CELL

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

(2013) Daniel Schulz et al.   CELL

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

The RNA Polymerase II C-terminal Domain-interacting Domain of Yeast Nrd1 Contributes to the Choice of Termination Pathway and Couples to RNA Processing by the Nuclear Exosome

(2013) Dong-hyuk Heo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dismantling Promoter-driven RNA Polymerase II Transcription Complexesin Vitroby the Termination Factor Rat1

(2013) Erika L. Pearson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Poly(A) Tail-Mediated Gene Regulation by Opposing Roles of Nab2 and Pab2 Nuclear Poly(A)-Binding Proteins in Pre-mRNA Decay

(2013) V. Grenier St-Sauveur et al.   MOLECULAR AND CELLULAR BIOLOGY

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Bimodal expression of PHO84 is modulated by early termination of antisense transcription

(2013) Manuele Castelnuovo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast

(2013) Odil Porrua et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human snRNA genes use polyadenylation factors to promote efficient transcription termination

(2013) Dawn O’Reilly et al.   NUCLEIC ACIDS RESEARCH

The Role of Ctk1 Kinase in Termination of Small Non-Coding RNAs

(2013) Tineke L. Lenstra et al.   PLoS One

Rrp47 functions in RNA surveillance and stable RNA processing when divorced from the exoribonuclease and exosome-binding domains of Rrp6

(2013) W. Garland et al.   RNA

High-Frequency Promoter Firing Links THO Complex Function to Heavy Chromatin Formation

(2013) John Mouaikel et al.   Cell Reports

Definition of RNA Polymerase II CoTC Terminator Elements in the Human Genome

(2013) Takayuki Nojima et al.   Cell Reports

Ubiquitylation and degradation of elongating RNA polymerase II: The last resort

(2012) Marcus D. Wilson et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Disengaging polymerase: Terminating RNA polymerase II transcription in budding yeast

(2012) Hannah E. Mischo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Transcription-associated histone modifications and cryptic transcription

(2012) Michaela Smolle et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Microprocessor, Setx, Xrn2, and Rrp6 Co-operate to Induce Premature Termination of Transcription by RNAPII

(2012) Alexandre Wagschal et al.   CELL

Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast

(2012) Folkert J. van Werven et al.   CELL

In vivoSELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination

(2012) Odil Porrua et al.   EMBO JOURNAL

The yeastRPL9Bgene is regulated by modulation between two modes of transcription termination

(2012) Rajani Kanth Gudipati et al.   EMBO JOURNAL

Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1

(2012) K. Kubicek et al.   GENES & DEVELOPMENT

The RNA polymerase II CTD coordinates transcription and RNA processing

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

Dynamic transitions in RNA polymerase II density profiles during transcription termination

(2012) A. R. Grosso et al.   GENOME RESEARCH

A Complex Containing the CPSF73 Endonuclease and Other Polyadenylation Factors Associates with U7 snRNP and Is Recruited to Histone Pre-mRNA for 3'-End Processing

(2012) X.-C. Yang et al.   MOLECULAR AND CELLULAR BIOLOGY

Ars2 Promotes Proper Replication-Dependent Histone mRNA 3′ End Formation

(2012) Joshua J. Gruber et al.   MOLECULAR CELL

Single-Cell Analysis Reveals that Noncoding RNAs Contribute to Clonal Heterogeneity by Modulating Transcription Factor Recruitment

(2012) Stacie L. Bumgarner et al.   MOLECULAR CELL

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

Rrp6p Controls mRNA Poly(A) Tail Length and Its Decoration with Poly(A) Binding Proteins

(2012) Manfred Schmid et al.   MOLECULAR CELL

A Universal RNA Polymerase II CTD Cycle Is Orchestrated by Complex Interplays between Kinase, Phosphatase, and Isomerase Enzymes along Genes

(2012) Alain R. Bataille et al.   MOLECULAR CELL

Extensive Degradation of RNA Precursors by the Exosome in Wild-Type Cells

(2012) Rajani Kanth Gudipati et al.   MOLECULAR CELL

Kinetic Competition between RNA Polymerase II and Sen1-Dependent Transcription Termination

(2012) Dane Z. Hazelbaker et al.   MOLECULAR CELL

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

CTD Tyrosine Phosphorylation Impairs Termination Factor Recruitment to RNA Polymerase II

(2012) A. Mayer et al.   SCIENCE

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Mpk1 MAPK Association with the Paf1 Complex Blocks Sen1-Mediated Premature Transcription Termination

(2011) Ki-Young Kim et al.   CELL

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

(2011) Wiebke Wlotzka et al.   EMBO JOURNAL

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

(2011) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

Unravelling the means to an end: RNA polymerase II transcription termination

(2011) Jason N. Kuehner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNAP II CTD Phosphorylated on Threonine-4 Is Required for Histone mRNA 3' End Processing

(2011) J.-P. Hsin et al.   SCIENCE

De Novo Origin of Human Protein-Coding Genes

(2011) Dong-Dong Wu et al.   PLoS Genetics

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

(2011) Tyler J. Creamer et al.   PLoS Genetics

Intergenic transcription causes repression by directing nucleosome assembly

(2010) S. J. Hainer et al.   GENES & DEVELOPMENT

A Subset of Drosophila Integrator Proteins Is Essential for Efficient U7 snRNA and Spliceosomal snRNA 3'-End Formation

(2010) N. Ezzeddine et al.   MOLECULAR AND CELLULAR BIOLOGY

Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription

(2010) A. N. Yadon et al.   MOLECULAR AND CELLULAR BIOLOGY

Gene-specific RNA polymerase II phosphorylation and the CTD code

(2010) Hyunmin Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chemical-genomic dissection of the CTD code

(2010) Joshua R Tietjen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain

(2010) Bradley M Lunde et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Uniform transitions of the general RNA polymerase II transcription complex

(2010) Andreas Mayer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

Transcription termination by nuclear RNA polymerases

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

Functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation

(2009) Amila Suraweera et al.   HUMAN MOLECULAR GENETICS

TorpedoNuclease Rat1 Is Insufficient to Terminate RNA Polymerase IIin Vitro

(2009) Stefan Dengl et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Yeast RNase III Triggers Polyadenylation-Independent Transcription Termination

(2009) Ghada Ghazal et al.   MOLECULAR CELL

Fail-Safe Transcriptional Termination for Protein-Coding Genes in S. cerevisiae

(2009) Ana G. Rondón et al.   MOLECULAR CELL

The Ess1 Prolyl Isomerase Is Required for Transcription Termination of Small Noncoding RNAs via the Nrd1 Pathway

(2009) Navjot Singh et al.   MOLECULAR CELL

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

A Novel Tandem Reporter Quantifies RNA Polymerase II Termination in Mammalian Cells

(2009) Ayan Banerjee et al.   PLoS One

Structure of Eukaryotic RNA Polymerases

(2008) P. Cramer et al.   Annual Review of Biophysics

Expression of human snRNA genes from beginning to end

(2008) Sylvain Egloff et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination

(2008) J. Kawauchi et al.   GENES & DEVELOPMENT

Properties of an Intergenic Terminator and Start Site Switch That Regulate IMD2 Transcription in Yeast

(2008) M. H. Jenks et al.   MOLECULAR AND CELLULAR BIOLOGY

Futile Cycle of Transcription Initiation and Termination Modulates the Response to Nucleotide Shortage in S. cerevisiae

(2008) Marilyne Thiebaut et al.   MOLECULAR CELL

Regulation of a Eukaryotic Gene by GTP-Dependent Start Site Selection and Transcription Attenuation

(2008) Jason N. Kuehner et al.   MOLECULAR CELL

The Glc7 Phosphatase Subunit of the Cleavage and Polyadenylation Factor Is Essential for Transcription Termination on snoRNA Genes

(2008) Eduard Nedea et al.   MOLECULAR CELL

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice

(2008) Rajani Kanth Gudipati et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain

(2008) Lidia Vasiljeva et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE