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

[1]  L. Steinmetz,et al.  Roadblock termination by reb1p restricts cryptic and readthrough transcription. , 2014, Molecular cell.

[2]  C. Moore,et al.  The evolutionarily conserved Pol II flap loop contributes to proper transcription termination on short yeast genes. , 2014, Cell reports.

[3]  J. Corden,et al.  Genome-Wide Mapping of Yeast RNA Polymerase II Termination , 2014, PLoS genetics.

[4]  J. Bähler,et al.  The RNA exosome promotes transcription termination of backtracked RNA polymerase II , 2014, Nature Structural &Molecular Biology.

[5]  Johannes Söding,et al.  Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition. , 2014, Molecular cell.

[6]  Konstantina Skourti-Stathaki,et al.  R-loops induce repressive chromatin marks over mammalian gene terminators , 2014, Nature.

[7]  P. Cramer,et al.  Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation , 2014, Molecular cell.

[8]  Nam Pho,et al.  A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription , 2014, Cell.

[9]  H. Handa,et al.  DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes , 2014, Nature Communications.

[10]  L. Tong,et al.  Delineating the Structural Blueprint of the Pre-mRNA 3′-End Processing Machinery , 2014, Molecular and Cellular Biology.

[11]  Judith B. Zaugg,et al.  Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast , 2014, Nucleic acids research.

[12]  D. O’Reilly,et al.  Human snRNA genes use polyadenylation factors to promote efficient transcription termination , 2013, Nucleic acids research.

[13]  P. Cramer,et al.  RNA polymerase II termination involves C-terminal-domain tyrosine dephosphorylation by CPF subunit Glc 7 , 2014 .

[14]  P. Kemmeren,et al.  The Role of Ctk1 Kinase in Termination of Small Non-Coding RNAs , 2013, PloS one.

[15]  X. Darzacq,et al.  High-frequency promoter firing links THO complex function to heavy chromatin formation. , 2013, Cell reports.

[16]  T. Jensen,et al.  CBC–ARS2 stimulates 3′-end maturation of multiple RNA families and favors cap-proximal processing , 2013, Nature Structural &Molecular Biology.

[17]  A. Hyman,et al.  The human cap-binding complex is functionally connected to the nuclear RNA exosome , 2013, Nature Structural &Molecular Biology.

[18]  T. Jensen,et al.  Dealing with pervasive transcription. , 2013, Molecular cell.

[19]  Daniel Schulz,et al.  Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis , 2013, Cell.

[20]  P. Cramer,et al.  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, The Journal of Biological Chemistry.

[21]  P. Mitchell,et al.  Rrp47 functions in RNA surveillance and stable RNA processing when divorced from the exoribonuclease and exosome-binding domains of Rrp6 , 2013, RNA.

[22]  A. Corbett,et al.  Poly(A) Tail-Mediated Gene Regulation by Opposing Roles of Nab2 and Pab2 Nuclear Poly(A)-Binding Proteins in Pre-mRNA Decay , 2013, Molecular and Cellular Biology.

[23]  David Tollervey,et al.  A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs , 2013, Cell.

[24]  Dirk Eick,et al.  The RNA polymerase II carboxy-terminal domain (CTD) code. , 2013, Chemical reviews.

[25]  L. Steinmetz,et al.  Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality , 2013, Nature Structural &Molecular Biology.

[26]  Daniel Zenklusen,et al.  Bimodal expression of PHO84 is modulated by early termination of antisense transcription , 2013, Nature Structural &Molecular Biology.

[27]  D. Libri,et al.  A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast , 2013, Nature Structural &Molecular Biology.

[28]  Christopher B. Burge,et al.  Promoter directionality is controlled by U1 snRNP and polyadenylation signals , 2013, Nature.

[29]  C. Moore,et al.  Dismantling Promoter-driven RNA Polymerase II Transcription Complexes in Vitro by the Termination Factor Rat1* , 2013, The Journal of Biological Chemistry.

[30]  N. Proudfoot,et al.  Definition of RNA Polymerase II CoTC Terminator Elements in the Human Genome , 2013, Cell reports.

[31]  S. Marquardt,et al.  Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination. , 2013, Molecular cell.

[32]  N. Proudfoot,et al.  Disengaging polymerase: Terminating RNA polymerase II transcription in budding yeast☆ , 2013, Biochimica et biophysica acta.

[33]  J. Workman,et al.  Transcription-associated histone modifications and cryptic transcription. , 2013, Biochimica et biophysica acta.

[34]  J. Svejstrup,et al.  Ubiquitylation and degradation of elongating RNA polymerase II: the last resort. , 2013, Biochimica et biophysica acta.

[35]  L. Steinmetz,et al.  Extensive degradation of RNA precursors by the exosome in wild-type cells. , 2012, Molecular cell.

[36]  Judith B. Zaugg,et al.  Gene Loops Enhance Transcriptional Directionality , 2012, Science.

[37]  Leighton J. Core,et al.  Defining the status of RNA polymerase at promoters. , 2012, Cell reports.

[38]  Z. Dominski,et al.  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, Molecular and Cellular Biology.

[39]  R. Stefl,et al.  In vivo SELEX reveals novel sequence and structural determinants of Nrd1‐Nab3‐Sen1‐dependent transcription termination , 2012, The EMBO journal.

[40]  J. Manley,et al.  The RNA polymerase II CTD coordinates transcription and RNA processing. , 2012, Genes & development.

[41]  B. Berkhout,et al.  Microprocessor, Setx, Xrn2, and Rrp6 Co-operate to Induce Premature Termination of Transcription by RNAPII , 2012, Cell.

[42]  Š. Vaňáčová,et al.  Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. , 2012, Genes & development.

[43]  Michael Primig,et al.  Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast , 2012, Cell.

[44]  L. Steinmetz,et al.  Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins. , 2012, Molecular cell.

[45]  Patrick Cramer,et al.  CTD Tyrosine Phosphorylation Impairs Termination Factor Recruitment to RNA Polymerase II , 2012, Science.

[46]  Maria Carmo-Fonseca,et al.  Dynamic transitions in RNA polymerase II density profiles during transcription termination , 2012, Genome research.

[47]  F. Feuerbach,et al.  The yeast RPL9B gene is regulated by modulation between two modes of transcription termination , 2012, The EMBO journal.

[48]  D. Bentley,et al.  mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. , 2012, Molecular cell.

[49]  Alexander van Oudenaarden,et al.  Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. , 2012, Molecular cell.

[50]  Pierre-Étienne Jacques,et al.  A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes. , 2012, Molecular cell.

[51]  J. Yong,et al.  Ars2 promotes proper replication-dependent histone mRNA 3' end formation. , 2012, Molecular cell.

[52]  D. Libri,et al.  Cryptic Transcription and Early Termination in the Control of Gene Expression , 2011, Genetics research international.

[53]  Amit P. Sheth,et al.  RNAP II CTD Phosphorylated on Threonine-4 Is Required for Histone mRNA 3′ End Processing , 2011, Science.

[54]  Ya-ping Zhang,et al.  De Novo Origin of Human Protein-Coding Genes , 2011, PLoS genetics.

[55]  Sarah J. Wheelan,et al.  Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1 , 2011, PLoS genetics.

[56]  S. Loeillet,et al.  XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast , 2011, Nature.

[57]  Konstantina Skourti-Stathaki,et al.  Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination , 2011, Molecular cell.

[58]  S. Marquardt,et al.  Distinct RNA degradation pathways and 3' extensions of yeast non-coding RNA species , 2011, Transcription.

[59]  C. Moore,et al.  Unravelling the means to an end: RNA polymerase II transcription termination , 2011, Nature Reviews Molecular Cell Biology.

[60]  D. Tollervey,et al.  The nuclear RNA polymerase II surveillance system targets polymerase III transcripts , 2011, The EMBO journal.

[61]  D. E. Levin,et al.  Mpk1 MAPK Association with the Paf1 Complex Blocks Sen1-Mediated Premature Transcription Termination , 2011, Cell.

[62]  J. Weissman,et al.  Nascent transcript sequencing visualizes transcription at nucleotide resolution , 2011, Nature.

[63]  Justin A. Pruneski,et al.  Intergenic transcription causes repression by directing nucleosome assembly. , 2011, Genes & development.

[64]  E. Wagner,et al.  A Subset of Drosophila Integrator Proteins Is Essential for Efficient U7 snRNA and Spliceosomal snRNA 3′-End Formation , 2010, Molecular and Cellular Biology.

[65]  J. Graber,et al.  Gene-specific RNA pol II phosphorylation and the "CTD code" , 2010, Nature Structural &Molecular Biology.

[66]  Johannes Söding,et al.  Uniform transitions of the general RNA polymerase II transcription complex , 2010, Nature Structural &Molecular Biology.

[67]  J. Delrow,et al.  Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription , 2010, Molecular and Cellular Biology.

[68]  Fan Yang,et al.  Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain , 2010, Nature Structural &Molecular Biology.

[69]  Xin Li,et al.  Chemical-genomic dissection of the CTD code , 2010, Nature Structural &Molecular Biology.

[70]  A. Jacquier.  The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs , 2009, Nature Reviews Genetics.

[71]  S. Buratowski.  Progression through the RNA polymerase II CTD cycle. , 2009, Molecular cell.

[72]  Olivia S. Beane,et al.  The Ess1 prolyl isomerase is required for transcription termination of small noncoding RNAs via the Nrd1 pathway. , 2009, Molecular cell.

[73]  Pierre-Étienne Jacques,et al.  Yeast RNase III triggers polyadenylation-independent transcription termination. , 2009, Molecular cell.

[74]  N. Proudfoot,et al.  Fail-Safe Transcriptional Termination for Protein-Coding Genes in S. cerevisiae , 2009, Molecular cell.

[75]  M. Lavin,et al.  Functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation. , 2009, Human molecular genetics.

[76]  Mimi C Sammarco,et al.  A Novel Tandem Reporter Quantifies RNA Polymerase II Termination in Mammalian Cells , 2009, PloS one.

[77]  P. Cramer,et al.  Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro* , 2009, The Journal of Biological Chemistry.

[78]  Patricia Richard,et al.  Transcription termination by nuclear RNA polymerases. , 2009, Genes & development.

[79]  H. Madhani,et al.  Mechanisms that Specify Promoter Nucleosome Location and Identity , 2009, Cell.

[80]  Christophe Malabat,et al.  Widespread bidirectional promoters are the major source of cryptic transcripts in yeast , 2009, Nature.

[81]  L. Steinmetz,et al.  Bidirectional promoters generate pervasive transcription in yeast , 2009, Nature.

[82]  Gene W. Yeo,et al.  Divergent Transcription from Active Promoters , 2008, Science.

[83]  Mikkel H. Schierup,et al.  RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters , 2008, Science.

[84]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[85]  D. Larson,et al.  Single-RNA counting reveals alternative modes of gene expression in yeast , 2008, Nature Structural &Molecular Biology.

[86]  B. Séraphin,et al.  Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae. , 2008, Molecular cell.

[87]  S. Buratowski,et al.  The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain , 2008, Nature Structural &Molecular Biology.

[88]  D. Libri,et al.  Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice , 2008, Nature Structural &Molecular Biology.

[89]  D. Brow,et al.  Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. , 2008, Molecular cell.

[90]  Sylvain Egloff,et al.  Expression of human snRNA genes from beginning to end. , 2008, Biochemical Society transactions.

[91]  P. Cramer,et al.  Structure of eukaryotic RNA polymerases. , 2008, Annual review of biophysics.

[92]  D. Reines,et al.  Properties of an Intergenic Terminator and Start Site Switch That Regulate IMD2 Transcription in Yeast , 2008, Molecular and Cellular Biology.

[93]  N. Proudfoot,et al.  Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. , 2008, Genes & development.

[94]  J. Greenblatt,et al.  The Glc7 phosphatase subunit of the cleavage and polyadenylation factor is essential for transcription termination on snoRNA genes. , 2008, Molecular cell.

[95]  D. Bentley,et al.  RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes , 2008, Nature Structural &Molecular Biology.

[96]  Oliver J. Rando,et al.  Chromatin remodelling at promoters suppresses antisense transcription , 2007, Nature.

[97]  A. Nag,et al.  The poly(A)-dependent transcriptional pause is mediated by CPSF acting on the body of the polymerase , 2007, Nature Structural &Molecular Biology.

[98]  H. Handa,et al.  NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs. , 2007, Molecular cell.

[99]  R. Ghirlando,et al.  Interaction of yeast RNA-binding proteins Nrd1 and Nab3 with RNA polymerase II terminator elements. , 2007, RNA.

[100]  O. Rando,et al.  Distinct pathways for snoRNA and mRNA termination. , 2006, Molecular cell.

[101]  Christopher L. Warren,et al.  Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. , 2006, Molecular cell.

[102]  J. Corden,et al.  Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. , 2006, Molecular cell.

[103]  D. Libri,et al.  Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. , 2006, Molecular cell.

[104]  N. Proudfoot,et al.  Pause Sites Promote Transcriptional Termination of Mammalian RNA Polymerase II , 2006, Molecular and Cellular Biology.

[105]  Arlen W. Johnson,et al.  The role of Rat1 in coupling mRNA 3'-end processing to transcription termination: implications for a unified allosteric-torpedo model. , 2006, Genes & development.

[106]  Sarah Ng,et al.  cis- and trans-Acting Determinants of Transcription Termination by Yeast RNA Polymerase II , 2006, Molecular and Cellular Biology.

[107]  S. Buratowski,et al.  Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts. , 2006, Molecular cell.

[108]  D. Gilmour,et al.  Pcf11 is a termination factor in Drosophila that dismantles the elongation complex by bridging the CTD of RNA polymerase II to the nascent transcript. , 2006, Molecular cell.

[109]  Fred Winston,et al.  in Saccharomyces cerevisiae , 2005 .

[110]  Mohamed-Ali Hakimi,et al.  Integrator, a Multiprotein Mediator of Small Nuclear RNA Processing, Associates with the C-Terminal Repeat of RNA Polymerase II , 2005, Cell.

[111]  Z. Dominski,et al.  The Polyadenylation Factor CPSF-73 Is Involved in Histone-Pre-mRNA Processing , 2005, Cell.

[112]  Jianhua Fu,et al.  CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11. , 2005, Genes & development.

[113]  B. Séraphin,et al.  Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase , 2005, Cell.

[114]  N. Proudfoot,et al.  Strong Polyadenylation and Weak Pausing Combine To Cause Efficient Termination of Transcription in the Human Gγ-Globin Gene , 2005, Molecular and Cellular Biology.

[115]  C. Cole,et al.  Yeast poly(A)-binding protein, Pab1, and PAN, a poly(A) nuclease complex recruited by Pab1, connect mRNA biogenesis to export. , 2005, Genes & development.

[116]  N. Proudfoot,et al.  Human 5′ → 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites , 2004, Nature.

[117]  N. Krogan,et al.  The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II , 2004, Nature.

[118]  I. Bozzoni,et al.  Coupling between snoRNP assembly and 3′ processing controls box C/D snoRNA biosynthesis in yeast , 2004, The EMBO journal.

[119]  N. Krogan,et al.  Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes , 2004, The EMBO journal.

[120]  S. Buratowski,et al.  Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing. , 2004, Molecular cell.

[121]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[122]  Lionel Minvielle-Sebastia,et al.  Pti1p and Ref2p found in association with the mRNA 3′ end formation complex direct snoRNA maturation , 2003, The EMBO journal.

[123]  W. Keller,et al.  Independent functions of yeast Pcf11p in pre‐mRNA 3′ end processing and in transcription termination , 2003, The EMBO journal.

[124]  Lionel Minvielle-Sebastia,et al.  Dual requirement for yeast hnRNP Nab2p in mRNA poly(A) tail length control and nuclear export , 2002, The EMBO journal.

[125]  Y. Osheim,et al.  EM visualization of Pol II genes in Drosophila: most genes terminate without prior 3′ end cleavage of nascent transcripts , 2002, Chromosoma.

[126]  D. Brow,et al.  RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts , 2001, Nature.

[127]  A. Fatica,et al.  Yeast snoRNA accumulation relies on a cleavage‐dependent/polyadenylation‐independent 3′‐processing apparatus , 2000, The EMBO journal.

[128]  R. Parker,et al.  Yeast Exosome Mutants Accumulate 3′-Extended Polyadenylated Forms of U4 Small Nuclear RNA and Small Nucleolar RNAs , 2000, Molecular and Cellular Biology.

[129]  P. Mitchell,et al.  Functions of the exosome in rRNA, snoRNA and snRNA synthesis , 1999, The EMBO journal.

[130]  N. Proudfoot,et al.  EM visualization of transcription by RNA polymerase II: downstream termination requires a poly(A) signal but not transcript cleavage. , 1999, Molecular cell.

[131]  K. Shigesada,et al.  Autogenous regulation of the gene for transcription termination factor rho in Escherichia coli: localization and function of its attenuators , 1986, Journal of bacteriology.