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Publications

Recent Publications:

2014

Sardana, R., Liu, X., Granneman, S., Zhu, J., Gill, M., Papoulas, O., Marcotte, E.M., Tollervey, D., Correll, C.C. and Johnson, A.W. (2015) The DEAH-box helicase Dhr1 Dissociates U3 from the pre-rRNA to promote formation of the Central Pseudoknot. PLoS Biol., in press.

Baßler, J., Paternoga, H., Holdermann, I., Thoms, M., Granneman, S., Barrio-Garcia, C., Nyarko, A., Stier, G., Clark, S.A., Schraivogel, D., Kallas, M., Beckmann, R., Tollervey, D., Barbar, E., Sinning, I. and Hurt, E. (2014) Structural insight into an essential assembly factor network on the preribosome. J. Cell Biol., pii: jcb.201408111.

El Hage, A., Webb, S., Kerr, A. and Tollervey, D. (2014) Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PLoS Gen., doi: pgen.1004716. PMID: 25357144

Turowski, T.W., Lebaron, S., Zhang, E., Peil, L., Dudnakova, T., Petfalski, E., Granneman, S., Rappsilber, J. and Tollervey, D. (2014) Rio1 mediates ATP-dependent final maturation of 40S ribosomal subunits. Nucleic Acids Res., 42, 12189-12199. PMID: 25294836

Leung, E., Schneider, C., Yan, F., Mohi-El-Din, H., Kudla, G., Tuck, A., Wlotzka, W., Doronina, V.A., Bartley, R., Watkins, N.J., Tollervey, D. and Brown, J.D. (2014) Integrity of SRP RNA is ensured by La and the nuclear RNA quality control machinery. Nucleic Acids Res. 42, 10698-10710.

Delan-Forino. C. and Tollervey, D. (2014) Lighting Up pre-mRNA Recognition. Mol. Cell, 55, 649-51. PMID: 25192362

Turowski, T.W. and Tollervey, D. (2014) Cotranscriptional events in eukaryotic ribosome synthesis. Wiley Interdiscip Rev RNA. doi: 10.1002/wrna.1263. PMID: 25176256

Tree, J.J., Granneman, S., McAteer, S.P., Tollervey, D. and Gally, D.L. (2014) Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherchia coli. Mol. Cell, 55, 199-213. PMID: 24910100

Loc’h, J., Blaud, M., Rety, S., Lebaron, S., Deschamps, P., Bareille, J., Jombart, J., Robert-Paganin, J., Delbos, L., Chardon, F., Zhang, E., Charenton, C., Tollervey, D. and Leulliot, N. (2014) RNA mimicry by the Fap7 adenylate kinase in ribosome biogenesis. PLoS Biol., 12, e1001860. PMID: 24823650

Booth, D.G., Takagi, M., Sanchez-Pulido, L., Petfalski, E., Vargiu, G., Samejima, K., Imamoto, N., Ponting, C.P., Tollervey, D., Earnshaw, W.C. and Vagnarell, P. (2014) Ki-67 is a PP1-interacting protein that organises the mitotic chromosome periphery. eLife3:e01641. PMID: 24867636

Ban, N., Beckmann, R., Cate, J.H., Dinman, J.D., Dragon, F., Ellis, S.R., Lafontaine, D.L., Lindahl, L., Liljas, A., Lipton, J.M., McAlear, M.A., Moore, P.B., Noller, H.F., Ortega, J., Panse, V.G., Ramakrishnan, V., Spahn, C.M., Steitz, T.A., Tchorzewski, M., Tollervey, D., Warren, A.J., Williamson, J.R., Wilson, D., Yonath, A., Yusupov, M. (2014) A new system for naming ribosomal proteins. Curr Opin Struct Biol., S0959-440X(14)00003-7. PMID: 24524803

García-Gómez, J.J., Fernández-Pevida, A., Lebaron, S., Rosado, I.V., Tollervey, D., Kressler, D. and de la Cruz, J. (2014) Final pre-40S Maturation Depends on the Functional Integrity of the 60S Subunit Ribosomal Protein L3. PLoS Genetics, 10(3):e1004205. doi: 10.1371/journal.pgen.1004205. PMID: 24603549

Axt, K., French, S.L., Beyer, A.L. and Tollervey D. (2014) Kinetic analysis demonstrates a requirement for the Rat1 exonuclease in cotranscriptional pre-rRNA cleavage. PLoS One, DOI: 10.1371/journal.pone.0085703. PMID: 24498264

Helwak, A. and Tollervey, D. (2014) Mapping the miRNA interactome by CLASH. Nature Protocols, 9, 711-728. PMID: 24577361

Schneider, C. and Tollervey, D. (2014) Looking into the barrel of the RNA exosome.
Nat Struct Mol Biol., 21, 17-18. PMID: 24389548

Matsuo, Y., Granneman, S., Thoms, M., Manikas, R-G. Tollervey, D. and Hurt, E. (2014) Coupled GTPase and remodeling ATPase activities form a check point for ribosome export. Nature, 505, 112-116. PMID: 24240281

Travis, A.J., Moody, J., Helwak, A., Tollervey, D. and Kudla, G. (2014) Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. Methods, S1046-2023(13)00418-0. PMID: 24211736

2013

Helwak, A., Kudla, G., Dudnakova, T., Tollervey, D. (2013) Mapping the human miRNA interactome by CLASH reveals frequent non-canonical binding. Cell 153, 654-665. PMID: 23622248

Lebaron, S., Segerstolpe, A., French, S.L., Dudnakova, T., de lima Alves, F Granneman, S., Rappsilber, J., Beyer, A.L., Wieslander, L. and Tollervey, D. (2013) Rrp5 binding at multiple sites coordinates pre-rRNA processing and assembly. Mol. Cell, 52 707-719.

Schneider, S. and Tollervey D. (2013) Threading the barrel of the RNA exosome. Trends Biochem. Sci. doi:pii: S0968-0004(13)00105-9. 10.1016/j.tibs.2013.06.013. PMID: 23910895

Segerstolpe, A., Granneman, S., Björk, P., de Lima Alves, F., Rappsilber, J., Andersson, C., Högbom, M., Tollervey, D. and Wieslander,  L. (2013) Multiple RNA interactions position Mrd1 at the site of the small subunit pseudoknot within the 90S pre-ribosome. Nucleic Acids Res., 41, 1178-1190. PMID: 23193268

Sloan, K.E., Mattijssen, S., Lebaron, S., Tollervey, D., Pruijn, G.J.M., Watkins N.J. (2013) Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human rRNA processing. J. Cell. Biol., 200, 577-588. PMID: 23439679

Travis, A.J., Moody, J., Helwak, A., Tollervey, D. and Kudla, G. (2013) Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. Methods, S1046-2023(13)00418-0.

Tuck, A. and Tollervey, D. (2013) Functions of Long Non-Coding RNAs in Non-mammalian. In: Systems Molecular Biology of Long Non-coding RNAs (Khalil, A. and Coller, J. Eds.) pp 137-162 (Springer).

Tuck, A.C. and Tollervey, D. (2013) A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell 154, 996-1009. PMID: 23993093

2012

Bradatsch, B,, Leidig, C., Granneman, S., Gnädig, M., Tollervey , D., Böttcher, B., Beckmann, R. and Hurt, E (2012) Structure of the late pre-60S subunit with nuclear export factor Arx1 bound at the exit tunnel. Nat. Struct. Mol. Biol. 19, 1234-1241.

Bohnsack, M.T., Tollervey, D. and Granneman, S. (2012) Identification of RNA helicase target sites by UV crosslinking and analysis of cDNA (CRAC). Meth. Enz. 511, 275-288.
 
Hahn, D., Kudla, G., Tollervey, D. and Beggs, J.D. (2012) Brr2p-mediated conformational rearrangements in the spliceosome during activation and substrate repositioning. Genes Dev. 26, 2408-2421.
 
Lebaron, S., Schneider, C., van Nues, R.W., Swiatkowska, A., Walsh, D., Böttcher, B,. Granneman, S., Watkins, N.J. and Tollervey, D. (2012) Proof reading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits. Nat. Struct. Mol. Biol. 19, 744-753.
 
Libri V, Helwak A, Miesen P, Santhakumar D, Borger JG, Kudla G, Grey F, Tollervey D, Buck AH. (2012) Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target. Proc. Natl. Acad. Sci. U.S.A.109, 279-284
 
Schneider, S., Kudla, G., Wlotzka, W., Tuck, A. and Tollervey, D. (2012) Transcriptome-wide Analysis of Exosome Targets. Mol. Cell,  48, 422-433
 
Swiatkowska, A., Wlotzka, W., Tuck, A., Barrass, J.D., Beggs J.D. and Tollervey, D. (2012) Kinetic analysis of pre-ribosome structure in vivo. RNA 18, 2187-2200

Tuck, A. and Tollervey, D. (2012) An RNA reset switch. Mol. Cell 45, 435-436.
 
2011
 
French, S.L., Sikes, M.L., Hontz, R.D., Osheim, Y.N., Lambert, T.E., El Hage, A., Smith, M.M., Tollervey, D., Smith, J.S. and Beyer, A.L. (2011) In yeast lacking Topoisomerase I, accumulation of hyper-negative topological stress in ribosomal RNA genes is enhanced by R-loop digestion. Mol. Cell. Biol., 31, 482-94.
 
Granneman S, Petfalski E, Tollervey D. (2011) A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease. EMBO J. 30, 4006-4019.
 
Houseley J, Tollervey D. (2011) Repeat expansion in the budding yeast ribosomal DNA can occur independently of the canonical homologous recombination machinery. Nucleic Acids Res. 39, 8778-8791.
 
Kudla, G., Granneman, S., Hahn, D., Beggs, J.D. and Tollervey, D. (2011) Crosslinking, ligation and sequencing of hybrids reveals novel snoRNA and snRNA interactions in yeast.  Proc. Natl. Acad. Sci. U.S.A., 108, 10010-10015.
 
Tuck A.C. and Tollervey, D. (2011) RNA in pieces. Trends Genet. 27, 422-432.
 
Mitchell P, Tollervey D. (2011) Finding the exosome. Adv Exp Med Biol. 702, 1-8.
 
van Nues, R.W., Granneman, S., Kudla, G., Sloan, K.E., Chicken, M., Tollervey, D.  and Watkins, N.J. Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing.  EMBO J., 30, 2420-2430.
 
Wlotzka, W., Kudla, G., Granneman, S., Tollervey, D. (2011) The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J., 30, 1790-1803.
 
2010
 
Alexander, R.D., Barrass, J.D., Dichtl, B., Kos, M., Obtulowicz, T., Robert, M.C., Koper, M., Karkusiewicz, I., Mariconti, L., Tollervey, D., Dichtl, B., Kufel, J., Bertrand, E., Beggs, J.D. (2010) RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae. RNA, 16, 2570-2580
 
El Hage, A., French, S.L., Beyer A.L. and Tollervey, D. (2010) Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev., 24,1546-58.
 
Kos, M. and Tollervey, D. (2010) Yeast Pre-rRNA Processing and Modification Occur Cotranscriptionally. Mol. Cell, 37, 809-820.
 
Granneman, S., Petfalski, E. Swiatkowska A. and Tollervey, D (2010) Cracking Pre-40S Ribosomal Subunit Structure by Systematic Analyses of RNA-Protein Cross-linking. EMBO J., 9, 2026-2036.
 
Houseley. J. and Tollervey, D. (2010) Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro". PLoS ONE, 5, e12271
 
Mitchell, P. and Tollervey, D. (2010) Finding the exosome. In RNA exosome. Ed. Torben Heick Jensen. Landes Bioscience.
http://www.landesbioscience.com/curie/chapter/4675/
 
Thomson E, Tollervey D. (2010) The final step in 5.8S rRNA processing is cytoplasmic in Saccharomyces cerevisiae. Mol. Cell. Biol. 30, 976-984.
 
2009
 
Bohnsack, M.T., Martin, R., Granneman, S., Ruprecht, M., Schleiff, E. and Tollervey, D (2009) Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis. Mol. Cell, 36, 583-592.
 
Granneman, S., Kudla, G., Petfalski, E. and Tollervey, D. (2009) Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high throughput analysis of cDNAs. Proc. Natl. Acad. Sci. U.S.A., 106, 9613-9818.
 
Houseley J, Tollervey D. (2009) The many pathways of RNA degradation. Cell, 136, 763-776.
 
Kudla, G., Murray, A.W., Tollervey, D. and Plotkin J.B. (2009) Coding sequence determinants of gene expression in Escherichia coli. Science, 324, 255-258.
 
Oeffinger, M., Zenklusen, D., Ferguson, A., Wei, K.E., El Hage, A., Tollervey, D., Chait, B.T., Singer, R.H., Rout, M.P. (2009) Rrp17p defines a new family of eukaryotic exonucleases required for 5’ end processing of pre-60S ribosomal RNA. Mol. Cell, 36, 768-781.
 
Schneider, C., Leung, E., Brown, J. and Tollervey, D. (2009) The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome. Nucleic Acids Res., 37, 1127-1140.
 
Skruzny, M., Schneider, C., Racz, A., Weng, J., Tollervey, D. and Hurt, E. (2009)
An endoribonuclease functionally linked to perinuclear mRNP quality control associates with the nuclear pore complexes. PLoS Biol., 7, e8.
 
Pertschy, P., Schneider, C., Gnädig, M., Schäfer, T., Tollervey, D. and Hurt, E. (2009) RNA helicase Prp43 and its co-factor Pfa1 promote 20S to 18S rRNA processing catalyzed by the endonuclease Nob1. J. Biol. Chem. 284, 35079-35091.
 
2008
 
Carneiro, T, Carvalho C, Braga J, Rino J, Milligan L, Tollervey D, Carmo-Fonseca M. (2008) Inactivation of Cleavage Factor I Components Rna14p and Rna15p Induces Sequestration of snoRNPs at Discrete Sites in the Nucleus. Mol. Biol. Cell 19, 1499-1508.
 
Ciais, D., Bohnsack, M.T. and Tollervey, D. (2008) The mRNA encoding the yeast ARE-binding protein Cth2 is generated by a novel 3' processing pathway. Nucleic Acids Res. 36: 3075-3084.
 
El Hage, A., Koper, M., Kufel J., and Tollervey, D (2008) Efficient termination of transcription by RNA polymerase I requires the 5’-exonuclease Rat1 in yeast. Genes Dev., 22,1069-1081.
 
Houseley J, Tollervey D. (2008) The nuclear RNA surveillance machinery: The link between ncRNAs and genome structure in budding yeast? Biochim Biophys Acta. 1779, 239-246.
 
Ciocchetta, F., Hillston, J., Kos, M. and Tollervey D. (2008) Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA. Theoretical Computer Science, 408, 41-54.
 
Milligan, L., Decourty, L., Saveanu, C., Rappsilber, J., Ceulemans, H., Jacquier, A. and Tollervey, D. (2008) A yeast exosome cofactor Mpp6 functions in RNA surveillance and in the degradation of ncRNA transcripts. Mol. Cell. Biol., 8, 5446-57.
 
Bohnsack, M.T., Kos, M. and Tollervey, D. (2008) Quantitative analysis of snoRNA association with pre-ribosomes and release of snR30 by Rok1 helicase. EMBO Rep. 9, 1230-1236
 
Houseley, J., Rubbi, L., Grunstein, M., Tollervey, D. and Vogelauer, M. (2008) A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol. Cell, 32, 685-695.