D Tollervey

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. pmc The mRNA encoding the yeast ARE-binding protein Cth2 is generated by a novel 3' processing pathway
    Delphine Ciais
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3JR, UK
    Nucleic Acids Res 36:3075-84. 2008
  2. pmc Yeast Rrp14p is required for ribosomal subunit synthesis and for correct positioning of the mitotic spindle during mitosis
    Marlene Oeffinger
    Wellcome Trust Centre for Cell Biology, University of Edinburgh Edinburgh EH9 3JR, Scotland, UK
    Nucleic Acids Res 35:1354-66. 2007
  3. pmc Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control
    Jonathan Houseley
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
    EMBO J 26:4996-5006. 2007
  4. pmc Rrp5 binding at multiple sites coordinates pre-rRNA processing and assembly
    Simon Lebaron
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland
    Mol Cell 52:707-19. 2013
  5. pmc A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs
    Alex Charles Tuck
    The University of Edinburgh, Wellcome Trust Centre for Cell Biology, Michael Swann Building, Kings Buildings, Edinburgh EH9 3JR, UK
    Cell 154:996-1009. 2013
  6. pmc Kinetic analysis demonstrates a requirement for the Rat1 exonuclease in cotranscriptional pre-rRNA cleavage
    Konstantin Axt
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland
    PLoS ONE 9:e85703. 2014
  7. pmc The nuclear RNA polymerase II surveillance system targets polymerase III transcripts
    Wiebke Wlotzka
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
    EMBO J 30:1790-803. 2011
  8. pmc Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits
    Simon Lebaron
    Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh, Scotland, UK
    Nat Struct Mol Biol 19:744-53. 2012
  9. pmc Transcriptome-wide analysis of exosome targets
    Claudia Schneider
    Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh UK
    Mol Cell 48:422-33. 2012
  10. pmc Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
    Aleksandra Helwak
    Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK
    Cell 153:654-65. 2013

Collaborators

Detail Information

Publications88

  1. pmc The mRNA encoding the yeast ARE-binding protein Cth2 is generated by a novel 3' processing pathway
    Delphine Ciais
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3JR, UK
    Nucleic Acids Res 36:3075-84. 2008
    ..We propose that CTH2 mRNA is processed from a 3'-extended primary transcript by the exosome, TRAMP and Nrd1/Nab3/Sen1 complexes. This unusual pathway may allow time for nuclear, ARE-mediated regulation of CTH2 levels involving Rat1...
  2. pmc Yeast Rrp14p is required for ribosomal subunit synthesis and for correct positioning of the mitotic spindle during mitosis
    Marlene Oeffinger
    Wellcome Trust Centre for Cell Biology, University of Edinburgh Edinburgh EH9 3JR, Scotland, UK
    Nucleic Acids Res 35:1354-66. 2007
    ..These data suggest that Rrp14p may play some role in cell polarity and/or spindle positioning, in addition to its function in ribosome synthesis...
  3. pmc Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control
    Jonathan Houseley
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
    EMBO J 26:4996-5006. 2007
    ..Co-transcriptional RNA binding by Trf4 may link RNA and DNA metabolism and direct immediate IGS1-R degradation by the exosome following transcription termination...
  4. pmc Rrp5 binding at multiple sites coordinates pre-rRNA processing and assembly
    Simon Lebaron
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland
    Mol Cell 52:707-19. 2013
    ..A key role in coordinating preribosomal assembly and processing was confirmed by chromatin spreads. Following depletion of Rrp5, cotranscriptional cleavage was lost and preribosome compaction greatly reduced...
  5. pmc A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs
    Alex Charles Tuck
    The University of Edinburgh, Wellcome Trust Centre for Cell Biology, Michael Swann Building, Kings Buildings, Edinburgh EH9 3JR, UK
    Cell 154:996-1009. 2013
    ..Our data also reveal the dynamic and heterogeneous nature of mRNA maturation, and highlight a subset of "lncRNA-like" mRNAs regulated by the nuclear surveillance machinery. ..
  6. pmc Kinetic analysis demonstrates a requirement for the Rat1 exonuclease in cotranscriptional pre-rRNA cleavage
    Konstantin Axt
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland
    PLoS ONE 9:e85703. 2014
    ..5 Kb past the A2 cleavage site. We speculate that assembly of early-acting 60S synthesis factors is monitored as a quality control system prior to NTC...
  7. pmc The nuclear RNA polymerase II surveillance system targets polymerase III transcripts
    Wiebke Wlotzka
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
    EMBO J 30:1790-803. 2011
    ..Surveillance targets were enriched for non-encoded A-rich tails. These were generally very short (1–5 nt), potentially explaining why adenylation destabilizes these RNAs while stabilizing mRNAs with long poly(A) tails...
  8. pmc Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits
    Simon Lebaron
    Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh, Scotland, UK
    Nat Struct Mol Biol 19:744-53. 2012
    ..We propose that recruitment of 60S subunits promotes GTP hydrolysis by Fun12, leading to structural rearrangements within the pre-40S particle that bring Nob1 and the pre-rRNA cleavage site together...
  9. pmc Transcriptome-wide analysis of exosome targets
    Claudia Schneider
    Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh UK
    Mol Cell 48:422-33. 2012
    ..Rrp6 was preferentially associated with structured targets, which frequently did not associate with the core exosome indicating that substrates follow multiple pathways to the nucleases...
  10. pmc Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
    Aleksandra Helwak
    Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK
    Cell 153:654-65. 2013
    ..We speculate that these affect the response of RISC to miRNA-target binding...
  11. pmc Yeast pre-rRNA processing and modification occur cotranscriptionally
    Martin Kos
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Mol Cell 37:809-20. 2010
    ..8S rRNAs was partially methylated on the nascent transcript. The results demonstrate that quantitative analyses of pre-rRNA processing can yield important biological insights...
  12. pmc Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis
    Markus T Bohnsack
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, UK
    Mol Cell 36:583-92. 2009
    ..We propose that Prp43 acts on preribosomal regions surrounding each binding site, with distinct functions at different locations...
  13. ncbi RNA-quality control by the exosome
    Jonathan Houseley
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
    Nat Rev Mol Cell Biol 7:529-39. 2006
    ..Recent studies now provide insights into the regulation and structure of the exosome, and they reveal striking similarities between the process of RNA degradation in bacteria and eukaryotes...
  14. ncbi Function and synthesis of small nucleolar RNAs
    D Tollervey
    Institute of Cell and Molecular Biology, University of Edinburgh, King s Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK
    Curr Opin Cell Biol 9:337-42. 1997
    ..Other groups of snoRNAs function in pre-rRNA cleavage and in the formation of the correct structure of the pre-rRNA...
  15. pmc Yeast Nop15p is an RNA-binding protein required for pre-rRNA processing and cytokinesis
    Marlene Oeffinger
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    EMBO J 22:6573-83. 2003
    ..In these late mitotic cells, Nop15p was partially delocalized from the nucleolus to the nucleoplasm, consistent with a specific function in cell division in addition to its role in ribosome synthesis...
  16. pmc The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases
    C Allmang
    Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR UK
    Genes Dev 13:2148-58. 1999
    ....
  17. ncbi The exosome subunit Rrp44 plays a direct role in RNA substrate recognition
    Claudia Schneider
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
    Mol Cell 27:324-31. 2007
    ..Recognition of hypomodified tRNA(i)(Met) by Rrp44 is genetically separable from its catalytic activity on other substrates, with the mutations mapping to distinct regions of the protein...
  18. ncbi Identification of a regulated pathway for nuclear pre-mRNA turnover
    C Bousquet-Antonelli
    Wellcome Trust Centre for Cell Biology ICMB, University of Edinburgh, Scotland
    Cell 102:765-75. 2000
    ..We propose that nuclear pre-mRNA turnover represents a novel step in the regulation of gene expression...
  19. pmc Nop58p is a common component of the box C+D snoRNPs that is required for snoRNA stability
    D L Lafontaine
    Institute of Cell and Molecular Biology, The University of Edinburgh, Scotland
    RNA 5:455-67. 1999
    ..Nop58p is the second common component of the box C+D snoRNPs to be identified and the first to be shown to be required for the stability and for the synthesis of these snoRNAs...
  20. ncbi RNA degradation by the exosome is promoted by a nuclear polyadenylation complex
    John LaCava
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Cell 121:713-24. 2005
    ..We speculate that this function was maintained in eukaryotic nuclei, while cytoplasmic mRNA poly(A) tails acquired different roles in translation...
  21. pmc Synthesis and assembly of the box C+D small nucleolar RNPs
    D L Lafontaine
    ICMB, The University of Edinburgh, Edinburgh EH9 3JR, Scotland
    Mol Cell Biol 20:2650-9. 2000
    ..Unexpectedly, we found that Nop1p was specifically required for the synthesis and accumulation of box C+D snoRNAs processed from pre-mRNA introns and polycistronic transcripts...
  22. pmc Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis?
    D L Lafontaine
    Institute of Cell and Molecular Biology, The University of Edinburgh, Scotland
    Mol Cell Biol 18:2360-70. 1998
    ..This observation, which demonstrates that Dim1p is not directly required for pre-rRNA processing reactions, is consistent with the inhibition of pre-rRNA processing by an active repression system in the absence of Dim1p...
  23. pmc Dhr1p, a putative DEAH-box RNA helicase, is associated with the box C+D snoRNP U3
    A Colley
    Institute of Cell and Molecular Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland
    Mol Cell Biol 20:7238-46. 2000
    ..We speculate that Dhr1p is targeted to the preribosomal particles by the U3-18S rRNA interaction and is required for the structural reorganization of the rRNA during formation of the central pseudoknot...
  24. pmc Processing of the precursors to small nucleolar RNAs and rRNAs requires common components
    E Petfalski
    Institute of Cell and Molecular Biology, University of Edinburgh, United Kingdom
    Mol Cell Biol 18:1181-9. 1998
    ..8S rRNA. Processing of the pre-rRNA and both intronic and polycistronic snoRNAs therefore involves common components...
  25. pmc Functions of the exosome in rRNA, snoRNA and snRNA synthesis
    C Allmang
    Institute of Cell and Molecular Biology, University of Edinburgh, Swann Building, King s Buildings, Edinburgh EH9 3JR, UK
    EMBO J 18:5399-410. 1999
    ..We conclude that the exosome is involved in the processing of many RNA substrates and that different components can have distinct functions...
  26. pmc The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase
    D L Lafontaine
    Institute of Cell and Molecular Biology, University of Edinburgh, King s Buildings, Edinburgh EH9 3JR, UK
    Genes Dev 12:527-37. 1998
    ..We conclude that Cbf5p is likely to be the rRNA Psi synthase and is an integral component of the box H + ACA class of snoRNPs, which function to target the enzyme to its site of action...
  27. pmc Naf1 p is a box H/ACA snoRNP assembly factor
    Alessandro Fatica
    Wellcome Trust Centre for Cell Biology, Swann Building, King s Buildings, University of Edinburgh, Edinburgh EH9 3JR, UK
    RNA 8:1502-14. 2002
    ..We propose that Naf1 p is recruited to the CTD of RNA polymerase II and binds to nascent box H/ACA snoRNAs promoting snoRNP assembly...
  28. pmc A nuclear surveillance pathway for mRNAs with defective polyadenylation
    Laura Milligan
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    Mol Cell Biol 25:9996-10004. 2005
    ..In wild-type strains, assembly of the cleavage and polyadenylation complex might be suboptimal at cryptic polyadenylation sites, causing slowed polyadenylation...
  29. pmc A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts
    Laura Milligan
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    Mol Cell Biol 28:5446-57. 2008
    ..Heterochromatic transcripts and other ncRNAs are characterized by very rapid degradation, and we predict that functional redundancy is an important feature of ncRNA metabolism...
  30. pmc Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae
    Christophe Dez
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
    EMBO J 25:1534-46. 2006
    ..Localization of pre-ribosomes to this focus was lost in sda1-2 strains lacking Trf4p or Rrp6p. We designate this nucleolar focus the No-body and propose that it represents a site of pre-ribosome surveillance...
  31. pmc Nop53p is required for late 60S ribosome subunit maturation and nuclear export in yeast
    Emma Thomson
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, Scotland
    RNA 11:1215-24. 2005
    ..The strong accumulation of preribosomes in the Nop53p-depleted strain further suggests that it may participate in targeting aberrant preribosomes to surveillance and degradation pathways...
  32. ncbi mRNA turnover
    P Mitchell
    Wellcome Trust Centre for Cell Biology, ICMB, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, UK
    Curr Opin Cell Biol 13:320-5. 2001
    ..Competition for the cap structure links translation and subsequent mRNA degradation, which may also involve multiple deadenylases...
  33. pmc Yeast Trf5p is a nuclear poly(A) polymerase
    Jonathan Houseley
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Swann Building, King s Buildings, Edinburgh EH9 3JR, UK
    EMBO Rep 7:205-11. 2006
    ..Trf5p co-purified with Mtr4p and Air1p, indicating that it forms a complex, designated TRAMP5, that has functions that partially overlap with the TRAMP complex...
  34. ncbi The Putative RNA Helicase Dbp4p Is Required for Release of the U14 snoRNA from Preribosomes in Saccharomyces cerevisiae
    Martin Kos
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    Mol Cell 20:53-64. 2005
    ..Point mutations in helicase motifs I and III of Dbp4p blocked release of U14 from preribosomes. We conclude that the helicase activity of Dbp4p is required to unwind U14 and snR41 from the pre-rRNA...
  35. pmc The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome
    Claudia Schneider
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Nucleic Acids Res 37:1127-40. 2009
    ..Finally, the N-terminal PIN domain was shown to be necessary and sufficient for association with the core exosome, indicating its dual function as a nuclease and structural element...
  36. pmc Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p
    Joanna Kufel
    Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
    Mol Cell Biol 22:5248-56. 2002
    ..These data are consistent with roles for an Lsm complex as a chaperone that facilitates the efficient association of pre-tRNA processing factors with their substrates...
  37. pmc Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex
    Joanna Kufel
    Wellcome Trust Centre for Cell Biology, King s Buildings, The University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    Mol Cell Biol 24:9646-57. 2004
    ..Nucleus-restricted mRNAs and pre-mRNA degradation intermediates that accumulate in lsm mutants remain 5' capped. We conclude that the Lsm2-8p complex normally targets nuclear RNA substrates for decapping...
  38. pmc A complex pathway for 3' processing of the yeast U3 snoRNA
    Joanna Kufel
    Institute of Cell and Molecular Biology, Swann Building, King s Buildings, The University of Edinburgh, Edinburgh EH9 3JR, UK
    Nucleic Acids Res 31:6788-97. 2003
    ..We propose that the Lsm2-8p complex functions as a chaperone in conjunction with Lhp1p to stabilise pre-U3 RNA species during 3' processing. The Sm complex may function as a back-up to stabilise 3' ends that are not protected by Lhp1p...
  39. pmc Yeast Pescadillo is required for multiple activities during 60S ribosomal subunit synthesis
    Marlene Oeffinger
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, United Kingdom
    RNA 8:626-36. 2002
    ..Nop7p is a component of at least three different pre-60S particles, and we propose that it carries out distinct functions in each of these complexes...
  40. ncbi Musing on the structural organization of the exosome complex
    P Mitchell
    Wellcome Trust Centre for Cell Biology, ICMB, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, UK
    Nat Struct Biol 7:843-6. 2000
    ..As no detailed structural data are yet available for the exosome complex, or any of its constituent enzymes, this discussion will rely heavily on rather speculative models...
  41. pmc Nob1p is required for cleavage of the 3' end of 18S rRNA
    Alessandro Fatica
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    Mol Cell Biol 23:1798-807. 2003
    ..This suggests that Nob1p accompanies the pre-40S ribosomes during nuclear export. Pre-40S export is not, however, inhibited by depletion of Nob1p...
  42. pmc Nop9 is an RNA binding protein present in pre-40S ribosomes and required for 18S rRNA synthesis in yeast
    Emma Thomson
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland
    RNA 13:2165-74. 2007
    ..The identification of Nop9p as a novel, essential factor in the nuclear maturation of 90S and pre-40S ribosomal subunits shows that the complement of ribosome synthesis factors remains incomplete...
  43. ncbi Lsm Proteins are required for normal processing and stability of ribosomal RNAs
    Joanna Kufel
    Wellcome Trust Centre for Cell Biology, Swann Building, King s Buildings, University of Edinburgh, United Kingdom
    J Biol Chem 278:2147-56. 2003
    ..We propose that Lsm proteins facilitate RNA protein interactions and structural changes required during ribosomal subunit assembly...
  44. ncbi Crosstalk between RNA metabolic pathways: an RNOMICS approach
    Jean D Beggs
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, King s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
    Nat Rev Mol Cell Biol 6:423-9. 2005
    ..This article describes the aims and results, to date, of the European RNOMICS project as an example of an integrated approach to investigate these links...
  45. ncbi Processing of 3'-extended read-through transcripts by the exosome can generate functional mRNAs
    Claire Torchet
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3JR Edinburgh, Scotland, UK
    Mol Cell 9:1285-96. 2002
    ..The balance between complete degradation of 3'-unprocessed pre-mRNAs and their processing to functional mRNAs is regulated, with degradation favored on glucose media...
  46. ncbi An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation
    Philip Mitchell
    Wellcome Trust Centre for Cell Biology, Institute for Cell and Molecular Biology, King s Buildings, University of Edinburgh, EH9 3JR, United Kingdom
    Mol Cell 11:1405-13. 2003
    ..We conclude that recognition of NMD substrates by the Upf surveillance complex can target mRNAs to rapid deadenylation and exosome-mediated degradation...
  47. pmc The final step in 5.8S rRNA processing is cytoplasmic in Saccharomyces cerevisiae
    Emma Thomson
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
    Mol Cell Biol 30:976-84. 2010
    ..We conclude that nuclear pre-60S particles containing the 6S pre-rRNA bind Nmd3 and Crm1 and are exported to the cytoplasm prior to final maturation by Ngl2...
  48. pmc Rrp47p is an exosome-associated protein required for the 3' processing of stable RNAs
    Philip Mitchell
    Wellcome Trust Centre for Cell Biology, Institute for Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    Mol Cell Biol 23:6982-92. 2003
    ..We propose that Rrp47p functions as a substrate-specific nuclear cofactor for exosome activity in the processing of stable RNAs...
  49. ncbi A surfeit of factors: why is ribosome assembly so much more complicated in eukaryotes than bacteria?
    Aziz El Hage
    Wellcome Trust Centre for Cell Biology, Edinburgh, Scotland, UK
    RNA Biol 1:10-5. 2004
    ..Here we will consider the differences between eukaryotic and bacterial ribosome synthesis that may underlie this distinction...
  50. pmc Efficient termination of transcription by RNA polymerase I requires the 5' exonuclease Rat1 in yeast
    Aziz El Hage
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    Genes Dev 22:1069-81. 2008
    ..When Rat1 catches Pol I, which is predicted to be paused at T1, transcription is terminated...
  51. pmc Roles of the HEAT repeat proteins Utp10 and Utp20 in 40S ribosome maturation
    Christophe Dez
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Scotland
    RNA 13:1516-27. 2007
    ..In the case of Utp10, 20S pre-rRNA synthesis was also modestly increased by this loss of surveillance activity...
  52. doi The nuclear RNA surveillance machinery: the link between ncRNAs and genome structure in budding yeast?
    Jonathan Houseley
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, UK
    Biochim Biophys Acta 1779:239-46. 2008
    ..Less well-understood observations link both the TRAMP and exosome complexes to chromatin structure and DNA repair, and we will speculate on the potential significance of these activities...
  53. pmc Quantitative analysis of snoRNA association with pre-ribosomes and release of snR30 by Rok1 helicase
    Markus T Bohnsack
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, King s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
    EMBO Rep 9:1230-6. 2008
    ..Dissociation of U3 and U14 from pre-ribosomes is also dependent on helicases, suggesting that release of the essential snoRNAs might differ mechanistically from release of the modification-guide snoRNAs...
  54. ncbi Microarray detection of novel nuclear RNA substrates for the exosome
    Rym Houalla
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3JR, UK
    Yeast 23:439-54. 2006
    ..Further analyses indicated that many snoRNA and snRNA genes are inefficiently terminated, but read-through transcripts into downstream ORFs are normally rapidly degraded by the exosome...
  55. pmc Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs
    Sander Granneman
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland
    Proc Natl Acad Sci U S A 106:9613-8. 2009
    ..This finding demonstrates that the snoRNP proteins directly contact the pre-rRNA substrate, suggesting roles in snoRNA recruitment. The techniques reported here should be widely applicable to analyses of RNA-protein interactions...
  56. ncbi mRNA stability in eukaryotes
    P Mitchell
    Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
    Curr Opin Genet Dev 10:193-8. 2000
    ..In yeast, the relationship between translation and mRNA turnover is clearer, but the mRNA decapping process has turned out to be unexpectedly complex...
  57. pmc FLIPing heterokaryons to analyze nucleo-cytoplasmic shuttling of yeast proteins
    Katsiaryna Belaya
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, United Kingdom
    RNA 12:921-30. 2006
    ....
  58. ncbi Making ribosomes
    Alessandro Fatica
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
    Curr Opin Cell Biol 14:313-8. 2002
    ..Around 140 identified, non-ribosomal proteins are currently implicated in post-transcriptional ribosome synthesis in yeast...
  59. pmc A pre-ribosome-associated HEAT-repeat protein is required for export of both ribosomal subunits
    Marlene Oeffinger
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
    Genes Dev 18:196-209. 2004
    ..We propose that Rrp12p binds to the RNA components of the pre-ribosomes and promotes export of both subunits via its interactions with the nucleoporins and Gsp1p...
  60. pmc 3'-processing of yeast tRNATrp precedes 5'-processing
    Joanna Kufel
    Wellcome Trust Centre for Cell Biology, King s Buildings, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
    RNA 9:202-8. 2003
    ..tRNA(Trp) is also unusual in not requiring Lhp1p for 3' processing and stability. However, other Lhp1p-independent tRNAs, tRNA(2)(Lys) and tRNA(1)(Ile), follow the normal pathway of 5'-processing prior to 3-processing...
  61. ncbi A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster
    Jonathan Houseley
    Wellcome Trust Centre for Cell Biology, Institute for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Mol Cell 32:685-95. 2008
    ..These chromatin modifications act principally through the Rpd3S complex to aid glucose repression of GAL1-10 at physiologically relevant sugar concentrations...
  62. pmc Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking
    Sander Granneman
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, UK
    EMBO J 29:2026-36. 2010
    ..Nob1 binds before pre-rRNA cleavage, and we conclude that structural reorganization is needed to bring together the catalytic PIN domain and its target...
  63. pmc RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae
    Ross D Alexander
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, King s Buildings, Edinburgh EH9 3JR, United Kingdom
    RNA 16:2570-80. 2010
    ..Using this approach, we demonstrate that reporter transcripts are spliced prior to their 3'-end cleavage and polyadenylation, that is, cotranscriptionally...
  64. pmc Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis
    Aziz El Hage
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
    Genes Dev 24:1546-58. 2010
    ..We conclude that the loss of Top1 enhances inherent R-loop formation, particularly over the 5' region of the rDNA, imposing persistent transcription blocks when RNase H is limiting...
  65. ncbi Ribosome synthesis meets the cell cycle
    Christophe Dez
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Curr Opin Microbiol 7:631-7. 2004
    ..The intersections between these pathways were not anticipated, but potential explanations for their existence can be advanced...
  66. ncbi The many pathways of RNA degradation
    Jonathan Houseley
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3JR, UK
    Cell 136:763-76. 2009
    ..Because RNA degradation is ubiquitous in all cells, it is clear that it must be carefully controlled to accurately recognize target RNAs. How this is achieved is perhaps the most pressing question in the field...
  67. ncbi 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors
    Paola Grandi
    Cellzome AG, Meyerhofstrasse 1, 69117, Heidelberg, Germany
    Mol Cell 10:105-15. 2002
    ..We conclude that the 40S synthesis machinery predominately associates with the 35S pre-rRNA factors, whereas factors required for 60S subunit synthesis largely bind later, showing an unexpected dichotomy in binding...
  68. pmc 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm
    Tracy A Nissan
    Biochemie Zentrum Heidelberg, Universitat Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
    EMBO J 21:5539-47. 2002
    ..As the 60S pre-ribosome reaches the cytoplasm, almost all of the factors are dissociated. These data provide an initial biochemical map of 60S ribosomal subunit formation on its path from the nucleolus to the cytoplasm...
  69. pmc Cic1p/Nsa3p is required for synthesis and nuclear export of 60S ribosomal subunits
    Alessandro Fatica
    Department of Genetics and Molecular Biology, University of Rome La Sapienza, Rome, Italy
    RNA 9:1431-6. 2003
    ..We suggest that Cic1p/Nsa3p associates early with nascent preribosomal particles and is required for correct processing and nuclear release of large ribosomal subunit precursors...
  70. ncbi A pre-ribosome with a tadpole-like structure functions in ATP-dependent maturation of 60S subunits
    Tracy A Nissan
    Biochemie Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, 69120, Germany
    Mol Cell 15:295-301. 2004
    ..Rea1 and the Rix1 complex could mediate ATP-dependent remodeling of 60S subunits and subsequent export from the nucleoplasm to the cytoplasm...
  71. pmc PIN domain of Nob1p is required for D-site cleavage in 20S pre-rRNA
    Alessandro Fatica
    Department of Genetics and Molecular Biology, University of Rome La Sapienza, Rome, Italy
    RNA 10:1698-701. 2004
    ..Cells expressing Nob1p with this mutation failed to cleave the 20S pre-rRNA. This supports both the significance of the structural model and the idea that Nob1p is the long-sought D-site endonuclease...
  72. ncbi Rea1, a dynein-related nuclear AAA-ATPase, is involved in late rRNA processing and nuclear export of 60 S subunits
    Kyriaki Galani
    Biochemie Zentrum der Universität Heidelberg BZH, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
    J Biol Chem 279:55411-8. 2004
    ..Using an in vivo 60 S subunit export assay, a strong accumulation of the large subunit reporter Rpl25-GFP (green fluorescent protein) in the nucleus and at the nuclear periphery was seen in rea1 mutants at restrictive conditions...
  73. pmc The path from nucleolar 90S to cytoplasmic 40S pre-ribosomes
    Thorsten Schäfer
    BZH, Universitat Heidelberg, Neuenheimer Feld 328, D 69120 Heidelberg, Germany
    EMBO J 22:1370-80. 2003
    ..Our data provide an initial biochemical map of the pre-40S ribosomal subunit on its path from the nucleolus to the cytoplasm. This pathway involves fewer changes in composition than seen during 60S biogenesis...
  74. pmc Rlp7p is associated with 60S preribosomes, restricted to the granular component of the nucleolus, and required for pre-rRNA processing
    Olivier Gadal
    BZH, Biochemie Zentrum Heidelberg, D 69120 Heidelberg, Germany
    J Cell Biol 157:941-51. 2002
    ..All together, these data suggest that pre-rRNA cleavage at site C2 specifically requires Rlp7p and occurs within pre-60S particles located in the GC region of the nucleolus...
  75. ncbi Molecular biology: termination by torpedo
    David Tollervey
    Nature 432:456-7. 2004
  76. pmc Depletion of the yeast nuclear exosome subunit Rrp6 results in accumulation of polyadenylated RNAs in a discrete domain within the nucleolus
    Tiago Carneiro
    Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, 1649 028 Lisbon, Portugal
    Mol Cell Biol 27:4157-65. 2007
    ..The accumulation of polyadenylated snoRNAs in a discrete nucleolar domain may promote their recognition as substrates for the exosome...
  77. ncbi Ssf1p prevents premature processing of an early pre-60S ribosomal particle
    Alessandro Fatica
    Wellcome Trust Centre for Cell Biology, United Kingdom
    Mol Cell 9:341-51. 2002
    ..This complex is distinct from recently reported pre-60S complexes in RNA and protein composition. We describe a multistep pathway of 60S preribosome maturation...
  78. ncbi Formation and nuclear export of preribosomes are functionally linked to the small-ubiquitin-related modifier pathway
    Vikram Govind Panse
    Biochemie Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
    Traffic 7:1311-21. 2006
    ..Together our data suggest that sumoylation of preribosomal particles in the nucleus and subsequent desumoylation at the NPC is necessary for efficient ribosome biogenesis and export in eukaryotes...
  79. ncbi Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit
    Thorsten Schäfer
    Biochemie Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
    Nature 441:651-5. 2006
    ..In vivo depletion of Hrr25 inhibits growth and leads to the accumulation of immature 40S subunits that contain unstably bound Rps3. We conclude that the kinase activity of Hrr25 regulates the maturation of 40S ribosomal subunits...
  80. ncbi Molecular biology: RNA lost in translation
    David Tollervey
    Nature 440:425-6. 2006
  81. ncbi Sen34p depletion blocks tRNA splicing in vivo and delays rRNA processing
    Viviana Volta
    Molecular Histology and Cell Growth, DiBiT HSR, 20132 Milan, Italy
    Biochem Biophys Res Commun 337:89-94. 2005
    ..Finally, we confirm that Tif6p accompanies 27S pre-rRNA maturation to 25S rRNA and we suggest that Sen34p endonuclease in Tif6p complex may affect also rRNA maturation...
  82. pmc Functional link between ribosome formation and biogenesis of iron-sulfur proteins
    Alexander Yarunin
    Biochemie Zentrum der Universität Heidelberg BZH, Heidelberg, Germany
    EMBO J 24:580-8. 2005
    ..Our data reveal an unexpected link between ribosome biogenesis and the biosynthetic pathway of cytoplasmic Fe-S proteins...
  83. pmc The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases
    Nicolas Leulliot
    Institut de Biochimie et de Biophysique Moleculaire et Cellulaire, UMR8619, Bat 430, Universite de Paris Sud, 91405 Orsay Cedex, France
    Nucleic Acids Res 36:629-39. 2008
    ..We conclude that the catalytic activity of Emg1 is not essential and that the presence of the protein is both necessary and sufficient for ribosome biogenesis...
  84. pmc The 'scavenger' m7GpppX pyrophosphatase activity of Dcs1 modulates nutrient-induced responses in yeast
    Naglis Malys
    Posttranscriptional Control Group, Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester M60 1QD, UK
    Nucleic Acids Res 32:3590-600. 2004
    ..We conclude that Dcs1 function influences cellular responses to changes in nutrient avialability, while Dcs2 seems to act as a modulator of Dcs1 function...
  85. pmc The Noc proteins involved in ribosome synthesis and export contain divergent HEAT repeats
    Mensur Dlakic
    RNA 10:351-4. 2004
    ..Because other HEAT-repeat proteins play key roles in transport processes, this finding provides a plausible mechanistic explanation for the function of the Noc proteins...
  86. pmc Fibrillarin is essential for early development and required for accumulation of an intron-encoded small nucleolar RNA in the mouse
    Kathryn Newton
    MRC Human Genetics Unit, Edinburgh EH4 2XU, United Kingdom
    Mol Cell Biol 23:8519-27. 2003
    ..However, the level of the intron-encoded box C/D snoRNA U76 was clearly reduced. This suggests a high requirement for snoRNA synthesis during an early stage in development...
  87. pmc Formation and nuclear export of tRNA, rRNA and mRNA is regulated by the ubiquitin ligase Rsp5p
    Silvia Neumann
    Biochemie Zentrum Heidelberg, Im Neuenheimer Feld 328, D 69120 Heidelberg, Germany
    EMBO Rep 4:1156-62. 2003
    ..These data implicate ubiquitination as a mechanism coordinating the major nuclear RNA biogenesis pathways...
  88. ncbi Insights into the structure and function of a guide RNP
    Alessandro Fatica
    Nat Struct Biol 10:237-9. 2003