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Items: 1 to 50 of 61

1.

Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges.

Beckmann BM, Granneman S.

Methods Mol Biol. 2019;2049:213-231. doi: 10.1007/978-1-4939-9736-7_13.

PMID:
31602614
2.

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.

Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM.

Nat Commun. 2019 Mar 1;10(1):990. doi: 10.1038/s41467-019-08942-3.

3.

High-Resolution, High-Throughput Analysis of Hfq-Binding Sites Using UV Crosslinking and Analysis of cDNA (CRAC).

Sy B, Wong J, Granneman S, Tollervey D, Gally D, Tree JJ.

Methods Mol Biol. 2018;1737:251-272. doi: 10.1007/978-1-4939-7634-8_15.

4.

An RNA-dependent mechanism for transient expression of bacterial translocation filaments.

Wang D, McAteer SP, Wawszczyk AB, Russell CD, Tahoun A, Elmi A, Cockroft SL, Tollervey D, Granneman S, Tree JJ, Gally DL.

Nucleic Acids Res. 2018 Apr 20;46(7):3366-3381. doi: 10.1093/nar/gky096.

5.

Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements.

Lackmann F, Belikov S, Burlacu E, Granneman S, Wieslander L.

Nucleic Acids Res. 2018 Apr 20;46(7):3692-3706. doi: 10.1093/nar/gky036.

6.

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination.

Choudhury NR, Heikel G, Trubitsyna M, Kubik P, Nowak JS, Webb S, Granneman S, Spanos C, Rappsilber J, Castello A, Michlewski G.

BMC Biol. 2017 Nov 8;15(1):105. doi: 10.1186/s12915-017-0444-9.

7.

High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast.

Burlacu E, Lackmann F, Aguilar LC, Belikov S, Nues RV, Trahan C, Hector RD, Dominelli-Whiteley N, Cockroft SL, Wieslander L, Oeffinger M, Granneman S.

Nat Commun. 2017 Sep 28;8(1):714. doi: 10.1038/s41467-017-00761-8.

8.

Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation.

Sharma S, Yang J, van Nues R, Watzinger P, Kötter P, Lafontaine DLJ, Granneman S, Entian KD.

PLoS Genet. 2017 May 24;13(5):e1006804. doi: 10.1371/journal.pgen.1006804. eCollection 2017 May.

9.

Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress.

van Nues R, Schweikert G, de Leau E, Selega A, Langford A, Franklin R, Iosub I, Wadsworth P, Sanguinetti G, Granneman S.

Nat Commun. 2017 Apr 11;8(1):12. doi: 10.1038/s41467-017-00025-5.

10.

Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments.

Selega A, Sirocchi C, Iosub I, Granneman S, Sanguinetti G.

Nat Methods. 2017 Jan;14(1):83-89. doi: 10.1038/nmeth.4068. Epub 2016 Nov 7.

PMID:
27819660
11.

The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection.

Lemay JF, Marguerat S, Larochelle M, Liu X, van Nues R, Hunyadkürti J, Hoque M, Tian B, Granneman S, Bähler J, Bachand F.

Genes Dev. 2016 Jul 1;30(13):1558-72. doi: 10.1101/gad.280222.116.

12.

Structure and activity of the anticaking agent iron(III) meso-tartrate.

Bode AA, Granneman SJ, Feiters MC, Verwer P, Jiang S, Meijer JA, van Enckevort WJ, Vlieg E.

Dalton Trans. 2016 Apr 21;45(15):6650-9. doi: 10.1039/c6dt00098c.

PMID:
26974191
13.

Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.

Holmes RK, Tuck AC, Zhu C, Dunn-Davies HR, Kudla G, Clauder-Munster S, Granneman S, Steinmetz LM, Guthrie C, Tollervey D.

PLoS Genet. 2015 Dec 22;11(12):e1005735. doi: 10.1371/journal.pgen.1005735. eCollection 2015 Dec.

14.

Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling.

Barrass JD, Reid JE, Huang Y, Hector RD, Sanguinetti G, Beggs JD, Granneman S.

Genome Biol. 2015 Dec 17;16:282. doi: 10.1186/s13059-015-0848-1.

15.

Regulation of mRNA Levels by Decay-Promoting Introns that Recruit the Exosome Specificity Factor Mmi1.

Kilchert C, Wittmann S, Passoni M, Shah S, Granneman S, Vasiljeva L.

Cell Rep. 2015 Dec 22;13(11):2504-2515. doi: 10.1016/j.celrep.2015.11.026. Epub 2015 Dec 6.

16.

Cell populations can use aneuploidy to survive telomerase insufficiency.

Millet C, Ausiannikava D, Le Bihan T, Granneman S, Makovets S.

Nat Commun. 2015 Oct 22;6:8664. doi: 10.1038/ncomms9664.

17.

A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation.

Baßler J, Paternoga H, Holdermann I, Thoms M, Granneman S, Barrio-Garcia C, Nyarko A, Lee W, Stier G, Clark SA, Schraivogel D, Kallas M, Beckmann R, Tollervey D, Barbar E, Sinning I, Hurt E.

J Cell Biol. 2015 Jul 6;210(1):169-70. doi: 10.1083/jcb.20140811106112015c. No abstract available.

18.

The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot.

Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW.

PLoS Biol. 2015 Feb 24;13(2):e1002083. doi: 10.1371/journal.pbio.1002083. eCollection 2015 Feb.

19.

A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation.

Baßler J, Paternoga H, Holdermann I, Thoms M, Granneman S, Barrio-Garcia C, Nyarko A, Lee W, Stier G, Clark SA, Schraivogel D, Kallas M, Beckmann R, Tollervey D, Barbar E, Sinning I, Hurt E.

J Cell Biol. 2014 Nov 24;207(4):481-98. doi: 10.1083/jcb.201408111. Epub 2014 Nov 17. Erratum in: J Cell Biol. 2015 Jul 6;210(1):169-70. Lee, Woonghee [added].

20.

Rio1 mediates ATP-dependent final maturation of 40S ribosomal subunits.

Turowski TW, Lebaron S, Zhang E, Peil L, Dudnakova T, Petfalski E, Granneman S, Rappsilber J, Tollervey D.

Nucleic Acids Res. 2014 Oct 29;42(19):12189-99. doi: 10.1093/nar/gku878. Epub 2014 Oct 7.

21.

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution.

Hector RD, Burlacu E, Aitken S, Le Bihan T, Tuijtel M, Zaplatina A, Cook AG, Granneman S.

Nucleic Acids Res. 2014 Oct 29;42(19):12138-54. doi: 10.1093/nar/gku815. Epub 2014 Sep 8.

22.

Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli.

Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL.

Mol Cell. 2014 Jul 17;55(2):199-213. doi: 10.1016/j.molcel.2014.05.006. Epub 2014 Jun 5.

23.

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast.

Webb S, Hector RD, Kudla G, Granneman S.

Genome Biol. 2014 Jan 7;15(1):R8. doi: 10.1186/gb-2014-15-1-r8.

24.

Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export.

Matsuo Y, Granneman S, Thoms M, Manikas RG, Tollervey D, Hurt E.

Nature. 2014 Jan 2;505(7481):112-116. doi: 10.1038/nature12731. Epub 2013 Nov 17.

25.

Rrp5 binding at multiple sites coordinates pre-rRNA processing and assembly.

Lebaron S, Segerstolpe A, French SL, Dudnakova T, de Lima Alves F, Granneman S, Rappsilber J, Beyer AL, Wieslander L, Tollervey D.

Mol Cell. 2013 Dec 12;52(5):707-19. doi: 10.1016/j.molcel.2013.10.017. Epub 2013 Nov 14.

26.

Spliceosome-mediated decay (SMD) regulates expression of nonintronic genes in budding yeast.

Volanakis A, Passoni M, Hector RD, Shah S, Kilchert C, Granneman S, Vasiljeva L.

Genes Dev. 2013 Sep 15;27(18):2025-38. doi: 10.1101/gad.221960.113.

27.

MLL2 mutation detection in 86 patients with Kabuki syndrome: a genotype-phenotype study.

Makrythanasis P, van Bon BW, Steehouwer M, Rodríguez-Santiago B, Simpson M, Dias P, Anderlid BM, Arts P, Bhat M, Augello B, Biamino E, Bongers EM, Del Campo M, Cordeiro I, Cueto-González AM, Cuscó I, Deshpande C, Frysira E, Izatt L, Flores R, Galán E, Gener B, Gilissen C, Granneman SM, Hoyer J, Yntema HG, Kets CM, Koolen DA, Marcelis Cl, Medeira A, Micale L, Mohammed S, de Munnik SA, Nordgren A, Psoni S, Reardon W, Revencu N, Roscioli T, Ruiterkamp-Versteeg M, Santos HG, Schoumans J, Schuurs-Hoeijmakers JH, Silengo MC, Toledo L, Vendrell T, van der Burgt I, van Lier B, Zweier C, Reymond A, Trembath RC, Perez-Jurado L, Dupont J, de Vries BB, Brunner HG, Veltman JA, Merla G, Antonarakis SE, Hoischen A.

Clin Genet. 2013 Dec;84(6):539-45. doi: 10.1111/cge.12081. Epub 2013 Apr 26.

PMID:
23320472
28.

Multiple RNA interactions position Mrd1 at the site of the small subunit pseudoknot within the 90S pre-ribosome.

Segerstolpe Å, Granneman S, Björk P, de Lima Alves F, Rappsilber J, Andersson C, Högbom M, Tollervey D, Wieslander L.

Nucleic Acids Res. 2013 Jan;41(2):1178-90. doi: 10.1093/nar/gks1129. Epub 2012 Nov 27.

29.

Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel.

Bradatsch B, Leidig C, Granneman S, Gnädig M, Tollervey D, Böttcher B, Beckmann R, Hurt E.

Nat Struct Mol Biol. 2012 Dec;19(12):1234-41. doi: 10.1038/nsmb.2438. Epub 2012 Nov 11.

30.

Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits.

Lebaron S, Schneider C, van Nues RW, Swiatkowska A, Walsh D, Böttcher B, Granneman S, Watkins NJ, Tollervey D.

Nat Struct Mol Biol. 2012 Aug;19(8):744-53. doi: 10.1038/nsmb.2308. Epub 2012 Jul 1.

31.

Identification of RNA helicase target sites by UV cross-linking and analysis of cDNA.

Bohnsack MT, Tollervey D, Granneman S.

Methods Enzymol. 2012;511:275-88. doi: 10.1016/B978-0-12-396546-2.00013-9.

PMID:
22713325
32.

A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease.

Granneman S, Petfalski E, Tollervey D.

EMBO J. 2011 Aug 2;30(19):4006-19. doi: 10.1038/emboj.2011.256.

33.

Genotype-phenotype correlation in DFNB8/10 families with TMPRSS3 mutations.

Weegerink NJ, Schraders M, Oostrik J, Huygen PL, Strom TM, Granneman S, Pennings RJ, Venselaar H, Hoefsloot LH, Elting M, Cremers CW, Admiraal RJ, Kremer H, Kunst HP.

J Assoc Res Otolaryngol. 2011 Dec;12(6):753-66. doi: 10.1007/s10162-011-0282-3. Epub 2011 Jul 23.

34.

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast.

Kudla G, Granneman S, Hahn D, Beggs JD, Tollervey D.

Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):10010-5. doi: 10.1073/pnas.1017386108. Epub 2011 May 24.

35.

Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing.

van Nues RW, Granneman S, Kudla G, Sloan KE, Chicken M, Tollervey D, Watkins NJ.

EMBO J. 2011 May 10;30(12):2420-30. doi: 10.1038/emboj.2011.148.

36.

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts.

Wlotzka W, Kudla G, Granneman S, Tollervey D.

EMBO J. 2011 May 4;30(9):1790-803. doi: 10.1038/emboj.2011.97. Epub 2011 Apr 1. Erratum in: EMBO J. 2011;30(14):2982.

37.

Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking.

Granneman S, Petfalski E, Swiatkowska A, Tollervey D.

EMBO J. 2010 Jun 16;29(12):2026-36. doi: 10.1038/emboj.2010.86. Epub 2010 May 7.

38.

Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis.

Bohnsack MT, Martin R, Granneman S, Ruprecht M, Schleiff E, Tollervey D.

Mol Cell. 2009 Nov 25;36(4):583-92. doi: 10.1016/j.molcel.2009.09.039.

39.

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs.

Granneman S, Kudla G, Petfalski E, Tollervey D.

Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9613-8. doi: 10.1073/pnas.0901997106. Epub 2009 May 29.

40.

Building ribosomes: even more expensive than expected?

Granneman S, Tollervey D.

Curr Biol. 2007 Jun 5;17(11):R415-7.

41.

The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis.

Granneman S, Lin C, Champion EA, Nandineni MR, Zorca C, Baserga SJ.

Nucleic Acids Res. 2006 Jun 13;34(10):3189-99. Print 2006.

42.

The PINc domain protein Utp24, a putative nuclease, is required for the early cleavage steps in 18S rRNA maturation.

Bleichert F, Granneman S, Osheim YN, Beyer AL, Baserga SJ.

Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9464-9. Epub 2006 Jun 12.

43.

Comprehensive mutational analysis of yeast DEXD/H box RNA helicases involved in large ribosomal subunit biogenesis.

Bernstein KA, Granneman S, Lee AV, Manickam S, Baserga SJ.

Mol Cell Biol. 2006 Feb;26(4):1195-208.

44.

Comprehensive mutational analysis of yeast DEXD/H box RNA helicases required for small ribosomal subunit synthesis.

Granneman S, Bernstein KA, Bleichert F, Baserga SJ.

Mol Cell Biol. 2006 Feb;26(4):1183-94.

45.
46.
47.

The small-subunit processome is a ribosome assembly intermediate.

Bernstein KA, Gallagher JE, Mitchell BM, Granneman S, Baserga SJ.

Eukaryot Cell. 2004 Dec;3(6):1619-26.

48.

RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components.

Gallagher JE, Dunbar DA, Granneman S, Mitchell BM, Osheim Y, Beyer AL, Baserga SJ.

Genes Dev. 2004 Oct 15;18(20):2506-17.

49.

Role of pre-rRNA base pairing and 80S complex formation in subnucleolar localization of the U3 snoRNP.

Granneman S, Vogelzangs J, Lührmann R, van Venrooij WJ, Pruijn GJ, Watkins NJ.

Mol Cell Biol. 2004 Oct;24(19):8600-10.

50.

Ribosome biogenesis: of knobs and RNA processing.

Granneman S, Baserga SJ.

Exp Cell Res. 2004 May 15;296(1):43-50. Review.

PMID:
15120992

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