Publications

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

Erika C. Urdaneta, Carlos H. Vieira-Vieira, Timon Hick, Hans-Herrmann Wessels, Davide Figini, Rebecca Moschall, Jan Medenbach, Uwe Ohler, Sander Granneman, Matthias Selbach & Benedikt M. Beckmann.

Nature Communications, 2019

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

Brandon Sy, Julia Wong, Sander Granneman, David Tollervey, David Gally and Jai J. Tree.

Methods in Molecular Biology, 2018. Volume 1737.

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

Dai Wang, Sean P. McAteer, Agata B. Wawszczyk, Clark D. Russell, Amin Tahoun, Alex Elmi, Scott L. Cockroft, David Tollervey, Sander Granneman, Jai J. Tree and David L. Gally.

Nucleic Acids Research, 2018 Feb 8.

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

Fredrik Lackmann, Sergey Belikov, Elena Burlacu, Sander Granneman and Lars Wieslander.

Nucleic Acids Research, 2018 Jan 24.

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

Nila Roy Choudhury, Gregory Heikel, Maryia Trubitsyna, Peter Kubik, Jakub Stanislaw Nowak, Shaun Webb, Sander Granneman, Christos Spanos, Juri Rappsilber, Alfredo Castello Palomares and Gracjan Michlewski.

BMC Biology, 2017; November 8 (15)

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

Elena Burlacu, Fredrik Lackmann, Lisbeth-Carolina Aguilar, Sergey Belikov, Rob van Nues, Christian Trahan, Ralph D. Hector, Nicholas Dominelli-Whiteley, Scott L. Cockroft, Lars Wieslander, Marlene Oeffinger and Sander Granneman#

Nature Communications, 2017

# corresponding author

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

Sunny Sharma, Jun Yang, Rob van Nues, Peter Watzinger, Peter Kötter, Denis LJ Lafontaine, Sander Granneman and Karl-Dieter Entian.

PLOS Genetics, 2017; May 24;13(5):e1006804.

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

Rob van Nues, Gabriele Schweikert, Erica de Leau, Alina Selega, Andrew Langford, Ryan Franklin, Ira Iosub, Peter Wadsworth, Guido Sanguinetti and Sander Granneman#

Nature Communications, 2017

# corresponding author

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

Alina Selega, Christel Sirocchi, Ira Iosub, Sander Granneman# & Guido Sanguinetti#.

Nature Methods, 2017; 14; 83-89.

# corresponding authors

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

Jean-François Lemay, Samuel Marguerat, Marc Larochelle, Xiaochuan Liu, Rob van Nues, Judit Hunyadkürti, Mainul Hoque, Bin Tian, Sander Granneman, Jürg Bähler and François Bachand.

Genes and Development, 2016; 30;1558-1572.

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

Rebecca K. Holmes, Alex C. Tuck, Chenchen Zhu, Hywel R. Dunn-Davies, Grzegorz Kudla, Sandra Clauder-Munster, Sander Granneman, Lars M Steinmetz, Christine Guthrie and David Tollervey.

Plos Genetics, 2015; 11

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

J. David Barass*, Jane E.A. Reid*, Yuanhua Huang*, Ralph D. Hector, Guido Sanguinetti, Jean D. Beggs# and Sander Granneman#.

Genome Biology, 2015; 16

# corresponding authors, *these authors contributed equally

Regulation of mRNA levels by suicidal introns that induce nuclear decay.

Cornelia Kilchert, Sina Wittman, Monica Passoni, Sneha Shah, Sander Granneman# and Lidia Vasiljeva#.

Cell Reports, 2015; 13, 1-12.

# corresponding authors

Cell populations can use aneuploidy to survive telomerase insufficiency

Caroline Millet, Darya Ausiannikava, Thierry Le Bihan, Sander Granneman, and Svetlana Makovets.

Nature Communications, 2015. 22;6:8664.

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

Richa Sardana, Xin Liu, Sander Granneman, Jieyi Zhu, Michael Gill, Ophelia Papoulas, Edward M Marcotte, David Tollervey, Carl Correll and Arlen W. Johnson.

PLOS Biology, 2015. 13(2):e1002083.

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

Jochen Baßler, Helge Paternoga, Iris Holdermann, Matthias Thoms, Sander Granneman, Clara Barrio-Garcia, Afua Nyarko, Gunther Stier, Sarah A. Clark, Daniel Schraivogel, Martina Kallas, Roland Beckmann, David Tollervey, Elisar Barbar, Irmi Sinning and Ed Hurt.

Journal of Cell Biology, 2014. 207(4):481-498.

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

Tomasz W. Turowski, Simon Lebaron, Elodie Zhang, Lauri Peil, Tatiana Dudnakova, Elisabeth Petfalski, Sander Granneman, Juri Rappsilber and David Tollervey.

Nucleic Acids Research 2014; 42(19):12189-12199.

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

Ralph D. Hector#, Elena Burlacu#, Stuart Aitken, Thierry Le Bihan, Maarten Tuijtel, Alina Zaplatina, Atlanta G. Cook and Sander Granneman.

Nucleic Acids Research 2014; 29;42(19):12138-12154.

# these authors contributed equally

Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli.

Jai J. Tree, Sander Granneman, Sean P. McAteer, David Tollervey, David L. Gally.

Molecular Cell, 2014; 55(2):199-213.

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

Shaun Webb, Ralph D. Hector, Grzegorz Kudla and Sander Granneman.

Genome Biology, 2014; 15:R8.

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

Yoshitaka Matsuo, Sander Granneman, Matthias Thoms, Rizos-Georgios Manikas, David Tollervey and Ed Hurt.

Nature, 2014; 505; 112-116.

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

Simon Lebaron, Åsa Segerstolpe, Sarah L. French, Tatiana Dudnakova, Flavia de lima Alves, Sander Granneman, Juri Rappsilber, Ann L. Beyer, Lars Wieslander and David Tollervey.

Molecular Cell 2013; 52(5):707-719.

Spliceosome-Mediated-Decay (SMD) regulates expression of non-intronic genes in budding yeast.

Adam Volanakis, Monica Passoni, Ralph D Hector, Sneha Shah, Cornelia Kilchert, Sander Granneman# and Lidia Vasiljeva#

Genes and Development 2013; 27(18):2025-2038.

# corresponding authors

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

Åsa Segerstolpe, Sander Granneman, Petra Björk, Flavia de Lima Alves, Juri Rappsilber, Charlotta Andersson, Martin Högbom, David Tollervey and Lars Wieslander.

Nucleic Acids Research 2013; 41(2):1178-1190.

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

Bettina Bradatsch, Christoph Leidig, Sander Granneman, Marén Gnädig, David Tollervey, Bettina Böttcher, Roland Beckmann and Ed Hurt.

Nature Structural and Molecular Biology, 2012; 19:1234-1241.

Identification of RNA Helicase Target Sites by UV Crosslinking and Analysis of cDNA (CRAC)

Markus Bohnsack, David Tollervey and Sander Granneman.

Methods in Enzymology 2012; 511:275-288.

Proof reading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits

Simon Lebaron, Claudia Schneider, Robert W. van Nues, Agata Swiatkowska, Dietrich Walsh, Bettina Böttcher, Sander Granneman, Nicholas J. Watkins and David Tollervey.

Nature Structural and Molecular Biology, 2012; 19(8):744-753.

A Cluster of Ribosome Synthesis Factors Regulate Pre-rRNA Folding and 5.8S rRNA Maturation by the Rat1 Exonuclease.

Sander Granneman#, Elisabeth Petfalski and David Tollervey#.

EMBO journal, 2011; 30(19):4006-4019.

# corresponding authors

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

Rob van Nues#, Sander Granneman#, Grzegorz Kudla, Katherine Elizabeth Sloan, Matthew Chicken, David Tollervey and Nicholas James Watkins.

EMBO journal, 2011; 30(12):2420-2430.

# these authors contributed equally

Mapping in vivo RNA-RNA interactions by crosslinking, ligation and sequencing of hybrids.

Grzegorz Kudla#, Sander Granneman#, Daniela Hahn#, Jean Beggs, and David Tollervey.

Proceedings of the National Academy of Sciences, 2011; 24; 10010-10015.

# these authors contributed equally

The Nuclear RNA Polymerase II Surveillance System Adds Short OligoA Tails and Targets Polymerase III Transcripts.

Wiebke Wlotzka, Grzegorz Kudla, Sander Granneman and David Tollervey.

EMBO journal, 2011; 9; 1790-1803.

Cracking Pre-40S ribosome Structure by Systematic Analyses of RNA-Protein Cross-linking. 2010.

Sander Granneman, Elisabeth Petfalski, Agata Swiatkovska and David Tollervey.

EMBO journal, 2010; 29; 2026-2036.

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

Markus T. Bohnsack, Roman Martin, Sander Granneman, Maike Ruprecht, Enrico Schleiff and David Tollervey.

Molecular Cell, 2009; 36; 583–592.

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

Sander Granneman, Grzegorz Kudla, Elisabeth Petfalski and David Tollervey.

Proceedings of the National Academy of Sciences, May 26, 2009; 24; 9613-9618.

Building ribosomes; Even more expensive than expected?

Sander Granneman and David Tollervey.

Current Biology, 2007; 17; 415-417.

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

Sander Granneman, ChieYu Lin, Erica A. Champion, Madhusudan R. Nandineni, Cornelia Zorca and Susan J. Baserga.

Nucleic Acids Research, 2006; 34; 3189-3199.

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

Franziska Bleichert, Sander Granneman, Yvonne N. Osheim, Ann L. Beyer, and Susan J. Baserga.

Proceedings of the National Academy of Sciences, 2006;24; 9464-9469.

A comprehensive mutational analysis of DEAD and DEAH box RNA helicases required for large ribosomal subunit biogenesis.

Kara Bernstein, Sander Granneman, Alicia Lee and Susan J. Baserga.

Molecular and Cellular Biology, 2006; 26; 1195-1208.

A comprehensive mutational analysis of DEAD and DEAH box RNA helicases required for SSU synthesis.

Sander Granneman, Kara Bernstein, Franziska Bleichert and Susan J. Baserga.

Molecular and Cellular Biology, 2006; 26; 1183-1194.

The putative ATPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14.

Sander Granneman, Madhusudan R. Nandineni and Susan J. Baserga.

Molecular and Cellular Biology, 2005; 25; 10352-10364.

Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing.

Sander Granneman and Susan J. Baserga.

Current Opinion in Cell Biology, 2005; 17; 281-286.

The SSU processome is a ribosome assembly intermediate.

Kara Bernstein, Jennifer E.G. Gallagher, Brianna M. Mitchell, Sander Granneman and Susan J. Baserga.

Eukaryotic Cell, 2004; 3; 1619-1626.

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

Jennifer E.G. Gallagher, David A. Dunbar, Sander Granneman, Brianna M. Mitchell, Yvonne Osheim, Ann L. Beyer and Susan J. Baserga.

Genes and Development, 2004; 18; 2506-2517.

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

Sander Granneman, Judith Vogelzangs, Reinhard Lührmann, Walther J. van Venrooij, Ger J.M. Pruijn and Nicholas J. Watkins.

Molecular and Cellular Biology, 2004; 24; 8600–8610.

Ribosome Biogenesis; of knobs and RNA processing.

Sander Granneman and Susan J. Baserga.

Experimental Cell Research, 2004; 296; 43-50.

Probing the yeast proteome for RNA processing factors.

Sander Granneman and Susan J. Baserga.

Genome Biology, 2003; 4; 229.

The human Imp3 and Imp4 proteins form a ternary complex with hMpp10, which only interacts with the U3 snoRNA in 60-80S ribonucleoprotein complexes.

Sander Granneman, Jenniffer E.G. Gallagher, Judith Vogelzangs, Wendy Horstman, Walther J. van Venrooij, Susan J. Baserga and Ger J.M. Pruijn.

Nucleic Acids Research, 2003; 31; 1877-1887.

The hU3-55K Protein Requires 15.5K Binding to the Box B/C Motif as Well as Flanking RNA Elements for Its Association with the U3 Small Nucleolar RNA in Vitro.

Sander Granneman, Ger J. M. Pruijn, Wendy Horstman, Walther J. van Venrooij, Reinhard Lührmann, and Nicholas J. Watkins.

Journal of Biological Chemistry, 2002; 227; 48490-48500.

Interaction of the U3-55k protein with U3 snoRNA is mediated by the box B/C motif of U3 and the WD repeats of U3-55k.

Andrew A. Lukowiak, Sander Granneman, Sharon A. Mattox, Wayne A. Speckmann, Kevin Jones, Helma Pluk, Walther J. van Venrooij, Rebecca M. Terns and Michael P. Terns.

Nucleic Acids Research, 2000 15; 28; 3462-71.

The Apoptosis-Promoting Factor TIA-1 Is a Regulator of Alternative Pre-mRNA Splicing.

Patrik Förch, Oscar Puig, Nancy Kedersha, Concepción Martínez, Sander Granneman, Bertrand Séraphin, Paul Anderson, and Juan Valcárcel.

Molecular Cell, 2000; 6; 1089-1098.

The roles of Rrp5p in the synthesis of yeast 18S and 5.8S rRNA can be functionally and physically separated.

Noor A. Eppens, Sietske Rensen, Sander Granneman, Hendrik A. Raue and Jaap Venema.

RNA, 1999; 5; 779-93.