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Publications

Recent Publications (numbers from full publication list):

2018 (to June)

251) McAteer, S.P., Sy, B.M., Wong J.L., Tollervey, D., Gally, D.L. and Tree, J.J. (2018) Ribosome maturation by the endoribonuclease YbeY stabilizes a type 3 secretion system transcript required for virulence of enterohemorrhagic Escherichia coli. J. Biol. Chem. 293. 9006-9016. PMID: 29678883

250) Bresson, S. and Tollervey, D. (2018) Tailing off: PABP and CNOT generate cycles of mRNA deadenylation. Mol. Cell, 70, 987–988.

249) Zuccotti, P., Tebaldi, T., Peroni, D., Köhn, M., Gasperini, L., Potrich, V., Dudnakova, T., Sanguinetti, G., Conti, L,. Macchi, P., Tollervey, D., Hüttelmaier, S. and Quattrone, A. (2018) HuD is a neural enhancer of global translation acting on mTORC1-responsive genes and sponged by the Y3 small non-coding RNA. Mol. Cell in press.

248) Bresson, S. and Tollervey, D. (2018) Surveillance-ready transcription: Nuclear RNA decay as a default fate. Open Biology. pii: 170270. doi: 10.1098/rsob.170270. PMID: 29563193

247) El Hage, A. and Tollervey, D. (2018) Immunoprecipitation of RNA:DNA Hybrids from Budding Yeast. Meth. Mol. Biol., 1703, 109-129. PMID: 29177737

246) Sy, B., Wong, J., Granneman, S., Tollervey, D., Gally, D. and Tree, J.J. (2018) High-resolution, high-throughput analysis of Hfq binding sites using UV-crosslinking and analysis of cDNA (CRAC). Meth. Mol. Biol., 1737, 251-272. PMID: 29484598

245) Wang, D., McAteer, S.P., Wawszczyk, A.B., Russell, C.D., Tahoun, A., Elmi, A., Cockroft, S.L., Tollervey, D., Granneman, S., Tree, J.T. and Gally D. (2018) An RNA-dependent mechanism for transient expression of bacterial translocation filaments Nucleic Acids Res., gky096. https://doi.org/10.1093/nar/gky096. PMID: 29432565

2017

244) Bharathavikru, R., Dudnakova, T., Aitken,S., Slight, J., Artibani, M.,Hohenstein, P., Tollervey, D. and Hastie, N. (2017) Transcription factor, Wilms’ Tumour 1 regulates developmental RNAs through 3’ UTR interaction. Genes Dev., 31, 347-352. PMCID: PMC5358755

243) Bresson, S., Tuck, A., Staneva, D. and Tollervey, D. (2017) Nuclear RNA decay pathways aid rapid remodeling of gene expression in yeast. Mol. Cell, 65, 787-800. PMCID: PMC5344683

242) Delan-Forino, C., Schneider, C. and Tollervey, D. (2017) Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex. PLoS Gen., 13, e1006699. PMCID:PMC5389853

241) Delan-Forino, C., Schneider, C. and Tollervey, D. (2017) RNA substrate length as an indicator of exosome interactions in vivo. Wellcome Open Res. doi: 10.12688/wellcomeopenres.10724.2 PMCID: PMC5500899

240) Milligan, L., Sayou, C., Tuck, A., Auchynnikava, T., Reid, J.E.A., Alexander, R., de Lima Alves, F., Allshire, R., Spanos, C., Rappsilber, J., Beggs, J.D. Kudla, G. and Tollervey, D. (2017) RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit. eLife, 6, e27082. PMCID:PMC5673307

239) Sayou, C., Millán-Zambrano, G., Santos-Rosa, H., Petfalski, E., Robson, S., Houseley, J., Kouzarides, T. and  Tollervey, D. (2017) RNA binding by the histone methyltransferases Set1 and Set2. Mol. Cell Biol. doi: 10.1128/MCB.00165-17. PMID: PMC28483910

238) Waters, S.A., McAteer,S.P., Kudla, G., Pang, I., Deshpande, N.P., Amos, T.G., Leong, K.W., Wilkins, M.R., Strugnell, R., Gally,D.L., Tollervey, D. and Tree, J.J. (2017) Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E. EMBO J. 36, 374-387. PMCID: PMC5286369

2016

237) Helwak, A. and Tollervey, D. (2016) Identification of miRNA-Target RNA Interactions Using CLASH. Methods Mol Biol. 1358, 229-251. PMID:26463387

236) Hunziker, M., Barandun, J., Petfalski, E., Tan, D., Delan-Forino, C., Molloy, K.R., Kim, K.H., Dunn-Davies, H., Shi, Y., Chaker-Margot, M., Chait, B.T., Walz, T., Tollervey, D. and Klinge, S. (2016) UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly. Nat. Commun., 7, 12090. PMCID: PMC4931317.

235) McCaughan, U.M., Jayachandran, U., Shchepachev, V., Chen, Z.A., Rappsilber, J., Tollervey, D. and Cook, A.G. (2016) Pre-40S ribosome biogenesis factor Tsr1 is an inactive structural mimic of translational GTPases. Nat. Comm., doi: 10.1038/ncomms11789. PMCID: PMC4895721

234) Milligan, L., Huynh-Thu, V.A., Delan-Forino, C., Tuck, A., Petfalski, E., Lombraña, R., Sanguinetti, G., Kudla, G. and Tollervey, D. (2016) Strand-specific, high-resolution mapping of modified RNA polymerase II. Mol. Syst. Biol.,12, 874. doi: 10.15252/msb.20166869. PMCID: PMC4915518

233) Puchta, O., Cseke, B., Czaja, H., Tollervey, D., Sanguinetti, G. and Kudla, G. (2016) Network of Epistatic Interactions Within a Yeast snoRNA. Science, 352, 840-844. PMCID: PMC5137784

232) Shchepachev, V. and Tollervey, D. (2016) Motoring toward pre-60S-ribosome export. Nat. Struct. Mol. Biol., 23, 3-4. PMID: 26733218*

231) Turowski TW, Tollervey D. (2016) Transcription by RNA polymerase III: insights into mechanism and regulation. Biochem. Soc. Trans., 44, 1367-1375. PMCID: PMC4937561

230) Turowski, T.W., Leśniewska, E., Delan-Forino, C., Sayou, C., Boguta, M., Tollervey, D. (2016) Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts. Genome Res., 26, 933-944. PMCID: PMC5095917

229) Winther, K., Tree, J.J., Tollervey, D. and Gerdes K. (2016) VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation. Nucleic Acids Res., doi: 10.1093/nar/gkw781. PMCID: PMC5175351

228) Wells, G.R, Weichmann, F., Colvin, D., Sloan, K.E., Kudla, G., Tollervey, D., Watkins, N.J. and Schneider, C. (2016) The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans. Nucleic Acids Res., 44, 5399-5409. PMCID: PMC5062985

2015

227) Holmes, R.K., Tuck, A.C., Zhu, C., Dunn-Davies, H.R., Kudla, G., Clauder-Munster, S., Granneman, S., Steinmetz, L.M., Guthrie, C. and Tollervey, D. (2015) Loss of the yeast SR protein Npl3 alters gene expression due to transcription readthrough. PLoS Gen., 11, e1005735. PMCID: PMC4687934

226) 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., 13:e1002083. PMCID: PMC4340053

225) Tollervey, D. (2015) RNA surveillance and the exosome. RNA, 21, 492-493 PMCID: PMC4371251*

2014

224) 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. PMCID: PMC3911906

223) 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. PMCID: PMC4358319*

222) 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) A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation. J. Cell Biol., 207, 481-498. PMCID: PMC4242840

221) 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. eLife, 3, e01641. PMCID: PMC4032110

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

219) 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., 10, e1004716. PMCID: PMC4214602

218) 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 Gen., 10, e1004205. PMCID: PMC3945201

217) Helwak, A. and Tollervey, D. (2014) Mapping the miRNA interactome by CLASH. Nature Protocols, 9, 711-728. PMCID: PMC4033841

216) 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. PMCID: PMC4176351

215) 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. PMCID: PMC4019466

214) 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. PMCID: PMC3880858

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

212) 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. PMCID: PMC3969109

211) 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. PMCID: PMC4104026

210) 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. PMCID: PMC4231747

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

2013

208) 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. PMCID: PMC3650559

207) 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. PMCID: PMC3991325

206) 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. PMCID: PMC3838930

205) 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. PMCID: PMC3553979

204) Sloan, K.E., Mattijssen, S., Lebaron, S., Tollervey, D., Pruijn, G.J.M. and Watkins N.J. (2013) Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human rRNA processing. J. Cell. Biol., 200, 577-588. PMCID: PMC3587827

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

202) 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. PMCID: PMC3778888