Liang-Cui ChuPedro Arede, Wei Li, Erika C. Urdaneta, Ivayla IvanovaStuart W. McKellar, Jimi Carlo Wills, Theresa Fröhlich, Alexander von Kriegsheim, Benedikt M. Beckmann and Sander Granneman#
The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins.
Nature Communications, 2022, in press.
# Corresponding author


Irina Kalita, Ira Alexandra Iosub, Sander Granneman, and Meriem El Karoui#. 
Fine-tuning of RecBCD expression by post-transcriptional regulation is required for optimal DNA repair in Escherichia coli
BioRxiv2021 DOIi: 2021
# Corresponding author
Stefan Gerhardy, Michaela Oborská-Oplová, Ludovic Gillet, Richard Börner, Rob van Nues, Alexander Leitner, Erich Michel, Janusz J. Petkowski, Sander Granneman, Roland K. O. Sigel, Ruedi Aebersold, Vikram Govind Panse.
Puf6 primes 60S pre-ribosome nuclear export at low temperature.
Nature Communications, 2021; 10.1038/s41467-021-24964-2
Paolo Marangio*, Ka Ying Toby Law*, Guido Sanguinetti# and Sander Granneman#.
diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data.
Genome Biology2021. PMCID: PMC8157727  DOI: 10.1186/s13059-021-02379-y
# corresponding authors
* These authors contributed equally
Gonzalo Yebra, Andreas F. Haag, Maan M. Neamah, Bryan A. WeeID1, Emily J. Richardson, Pilar Horcajo, Sander Granneman, Maria Ángeles Tormo-Mas, Ricardo de la Fuente, J. Ross Fitzgerald, José R. Penadés.
Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen.
PLoS Pathog 17(5): e1009606. journal.ppat.1009606
Niki Christopoulou and Sander Granneman.
The role of RNA‐binding proteins in mediating adaptive responses in Gram‐positive bacteria
The FEBS Journal; DOI:


Ira A. Iosub, Marta Marchioretto, Rob W. van Nues, Stuart W. McKellar, Gabriella Viero and Sander Granneman.
The mRNA derived MalH sRNA contributes to alternative carbon source utilization by tuning maltoporin expression in E. coli.
RNA Biology; DOI: 10.1080/15476286.2020.1827784
Ira A. Iosub, Rob W. van Nues, Stuart W. McKellar, Karen J. Nieken, Marta Marchioretto, Brandon Sy, Jai J. Tree, Gabriella Viero and Sander Granneman.
Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation. eLIFE, 2020;9:e54655 DOI: 10.7554/eLife.54655
Stuart W. McKellar, Ivayla Ivanova, Robert W. van Nues, Ross A. Cordiner, Will Worboys, Andrew Langford, Torben Heick Jensen and Sander Granneman.
Monitoring Protein-RNA Interaction Dynamics in vivo at High Temporal Resolution Using χCRAC. J. Vis. Exp., 2020; May 9;(159) DOI: 10.3791/61027.


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 .
Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.
Nature Communications, 2019; doi:10.1038/s41467-019-08942-3


Brandon Sy, Julia Wong, Sander Granneman, David Tollervey, David Gally and Jai J. Tree.
High-Resolution, High-Throughput Analysis of Hfq-Binding Sites Using UV Crosslinking and Analysis of cDNA (CRAC)
Methods in Molecular Biology, 2018. Volume 1737
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.
An RNA-dependent mechanism for transient expression of bacterial translocation filaments
Nucleic Acids Research, 2018 Feb 8. doi: 10.1093/nar/gky096. [Epub ahead of print]
Fredrik Lackmann, Sergey Belikov, Elena Burlacu, Sander Granneman and Lars Wieslander.
Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements.
Nucleic Acids Research,  2018 Jan 24. doi: 10.1093/nar/gky036. [Epub ahead of print]


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.
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination.
BMC Biology, 2017; November 8 (15) doi: 10.1186/s12915-017-0444-9.
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#
High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast.
Nature Communications, 2017; doi:10.1038/s41467-017-00761-8
# corresponding author
Sunny Sharma, Jun Yang, Rob van Nues, Peter Watzinger, Peter Kötter, Denis LJ Lafontaine, Sander Granneman and Karl-Dieter Entian.
Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation.
PLOS Genetics, 2017; May 24;13(5):e1006804. doi: 10.1371/journal.pgen.1006804
Rob van Nues, Gabriele Schweikert, Erica de Leau, Alina Selega, Andrew Langford, Ryan Franklin, Ira Iosub, Peter Wadsworth, Guido Sanguinetti and Sander Granneman#
Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress.
Nature Communications, 2017; DOI: 10.1038/s41467-017-00025-5
# corresponding author
Alina Selega, Christel Sirocchi, Ira Iosub, Sander Granneman# & Guido Sanguinetti#.
Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments.
Nature Methods, 2017; 14; 83-89.
# corresponding authors


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.
The Nrd1-like protein Seb1 coordinates cotranscriptional 3′ end processing and polyadenylation site selection.
Genes and Development, 2016; 30;1558-1572



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.
Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.
Plos Genetics, 2015; 11; DOI: 10.1371/journal.pgen.1005735.
J. David Barass*, Jane E.A. Reid*, Yuanhua Huang*, Ralph D. Hector, Guido Sanguinetti, Jean D. Beggs# and Sander Granneman#.
Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling.
Genome Biology, 2015; 16; DOI: 10.1186/s13059-015-0848-1
# corresponding authors, *these authors contributed equally
Cornelia Kilchert, Sina Wittman, Monica Passoni, Sneha Shah, Sander Granneman# and Lidia Vasiljeva#.
Regulation of mRNA levels by suicidal introns that induce nuclear decay.
Cell Reports, 2015; 13, 1-12.
# corresponding authors
Caroline Millet, Darya Ausiannikava, Thierry Le Bihan, Sander Granneman, and Svetlana Makovets.
Cell populations can use aneuploidy to survive telomerase insufficiency
Nature Communications, 2015. 22;6:8664.
Richa Sardana, Xin Liu, Sander Granneman, Jieyi Zhu, Michael Gill, Ophelia Papoulas, Edward M Marcotte, David Tollervey, Carl Correll and Arlen W. Johnson.
The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot.
PLOS Biology, 2015. 13(2):e1002083.



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.
A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation.
Journal of Cell Biology, 2014. 207(4):481-498
Tomasz W. Turowski, Simon Lebaron, Elodie Zhang, Lauri Peil, Tatiana Dudnakova, Elisabeth Petfalski, Sander Granneman, Juri Rappsilber and David Tollervey.
Rio1 mediates ATP-dependent final maturation of 40S ribosomal subunits.
Nucleic Acids Research 2014; 42(19):12189-12199
Ralph D. Hector#, Elena Burlacu#, Stuart Aitken, Thierry Le Bihan, Maarten Tuijtel, Alina Zaplatina, Atlanta G. Cook and Sander Granneman.
Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution.
Nucleic Acids Research 2014; 29;42(19):12138-12154
# these authors contributed equally
Jai J. Tree, Sander Granneman, Sean P. McAteer, David Tollervey, David L. Gally.
Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli.
Molecular Cell, 2014; 505(7481):112-116
Shaun Webb, Ralph D. Hector, Grzegorz Kudla and Sander Granneman.
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast.
Genome Biology, 2014;15:R8 
Yoshitaka Matsuo, Sander Granneman, Matthias Thoms, Rizos-Georgios Manikas, David Tollervey and Ed Hurt.
Coupled GTPase and remodeling ATPase activities form a checkpoint for ribosome export.
Nature, 2014; 505; 112-116



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.
Rrp5 binding at multiple sites coordinates pre-rRNA processing and assembly.
Molecular Cell 2013; Nov 12. doi:pii: S1097-2765
Adam Volanakis, Monica Passoni, Ralph D Hector, Sneha Shah, Cornelia Kilchert, Sander Granneman# and Lidia Vasiljeva#
Spliceosome-Mediated-Decay (SMD) regulates expression of non-intronic genes in budding yeast.
Genes and Development 2013; 18; 2025-38
# corresponding authors
Åsa Segerstolpe, Sander Granneman, Petra Björk, Flavia de Lima Alves, Juri Rappsilber, Charlotta Andersson, Martin Högbom, David Tollervey and Lars Wieslander.
Multiple RNA interactions position Mrd1 at the site of small subunit pseudoknot within the 90S pre-ribosome.
Nucleic Acids Research 2013; 2:1178-90.



Bettina Bradatsch, Christoph Leidig, Sander Granneman, Marén Gnädig, David Tollervey, Bettina Böttcher, Roland Beckmann and Ed Hurt.
Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel
Nature Structural and Molecular Biology, 2012;12:1234-41
Markus Bohnsack, David Tollervey and Sander Granneman.
Identification of RNA Helicase Target Sites by UV Crosslinking and Analysis of cDNA (CRAC)
Methods in Enzymology 2012; 511:275-88.
Simon Lebaron, Claudia Schneider, Robert W. van Nues, Agata Swiatkowska, Dietrich Walsh, Bettina Böttcher, Sander Granneman, Nicholas J. Watkins and David Tollervey.
Proof reading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits
Nature Structural and Molecular Biology, 2012; 8:744-53



Sander Granneman#, Elisabeth Petfalski and David Tollervey#.
A Cluster of Ribosome Synthesis Factors Regulate Pre-rRNA Folding and 5.8S rRNA Maturation by the Rat1 Exonuclease.
EMBO journal, 2011; 19; 4006-4019
# corresponding authors
Rob van Nues#, Sander Granneman#, Grzegorz Kudla, Katherine Elizabeth Sloan, Matthew Chicken, David Tollervey and Nicholas James Watkins.
Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing.
EMBO journal, 2011; 12; 2420-2430
# these authors contributed equally
Grzegorz Kudla#, Sander Granneman#, Daniela Hahn#, Jean Beggs, and David Tollervey.
Mapping in vivo RNA-RNA interactions by crosslinking, ligation and sequencing of hybrids.
Proceedings of the National Academy of Sciences, 2011; 24; 10010-10015
# these authors contributed equally
Wiebke Wlotzka, Grzegorz Kudla, Sander Granneman and David Tollervey.
The Nuclear RNA Polymerase II Surveillance System Adds Short OligoA Tails and Targets Polymerase III Transcripts.
EMBO journal, 2011; 9; 1790-1803



Sander Granneman, Elisabeth Petfalski, Agata Swiatkovska and David Tollervey.
Cracking Pre-40S ribosome Structure by Systematic Analyses of RNA-Protein Cross-linking. 2010.
EMBO journal, 2010; 29; 2026-2036


Markus T. Bohnsack, Roman Martin, Sander Granneman, Maike Ruprecht, Enrico Schleiff and David Tollervey.
Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis.
Molecular Cell, 2009; 36; 583–592
Sander Granneman, Grzegorz Kudla, Elisabeth Petfalski and David Tollervey.
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high throughput analysis of cDNAs
Proceedings of the National Academy of Sciences, May 26, 2009; 24; 9613-9618



Sander Granneman and David Tollervey.
Building ribosomes; Even more expensive than expected?
Current Biology, 2007; 17; 415-417


Sander Granneman, ChieYu Lin, Erica A. Champion, Madhusudan R. Nandineni, Cornelia Zorca and Susan J. Baserga.
The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis.
Nucleic Acids Research, 2006; 34; 3189-3199.
Franziska Bleichert, Sander Granneman, Yvonne N. Osheim, Ann L. Beyer, and Susan J. Baserga.
The PINc domain protein Utp24, a putative nuclease, is required for the early cleavage steps in 18S rRNA maturation.
Proceedings of the National Academy of Sciences, 2006;24; 9464-9469
Kara Bernstein, Sander Granneman, Alicia Lee and Susan J. Baserga.
A comprehensive mutational analysis of DEAD and DEAH box RNA helicases required for large ribosomal subunit biogenesis.
Molecular and Cellular Biology, 2006; 26; 1195-1208.
Sander Granneman, Kara Bernstein, Franziska Bleichert and Susan J. Baserga.
A comprehensive mutational analysis of DEAD and DEAH box RNA helicases required for SSU synthesis.
Molecular and Cellular Biology, 2006; 26; 1183-1194.



Sander Granneman, Madhusudan R. Nandineni and Susan J. Baserga.
The putative ATPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14.
Molecular and Cellular Biology, 2005; 25; 10352-10364.
Sander Granneman and Susan J. Baserga.
Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing.
Current Opinion in Cell Biology, 2005; 17; 281-286.



Kara Bernstein, Jennifer E.G. Gallagher, Brianna M. Mitchell, Sander Granneman and Susan J. Baserga.
The SSU processome is a ribosome assembly intermediate.
Eukaryotic Cell, 2004; 3; 1619-1626.
Jennifer E.G. Gallagher, David A. Dunbar, Sander Granneman, Brianna M. Mitchell, Yvonne Osheim, Ann L. Beyer and Susan J. Baserga.
RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components.
Genes and Development, 2004; 18; 2506-2517.
Sander Granneman, Judith Vogelzangs, Reinhard Lührmann, Walther J. van Venrooij, Ger J.M. Pruijn and Nicholas J. Watkins.
Role of pre-rRNA base-pairing and 80S complex formation in subnucleolar localisation of the U3 snoRNP.
Molecular and Cellular Biology, 2004; 24; 8600–8610
Sander Granneman and Susan J. Baserga.
Ribosome Biogenesis; of knobs and RNA processing.
Experimental Cell Research, 2004; 296; 43-50



Sander Granneman and Susan J. Baserga.
Probing the yeast proteome for RNA processing factors.
Genome Biology, 2003; 4; 229.
Sander Granneman, Jenniffer E.G. Gallagher, Judith Vogelzangs, Wendy Horstman, Walther J. van Venrooij, Susan J. Baserga and Ger J.M. Pruijn.
The human Imp3 and Imp4 proteins form a ternary complex with hMpp10, which only interacts with the U3 snoRNA in 60-80S ribonucleoprotein complexes.
Nucleic Acids Research, 2003; 31; 1877-1887



Sander Granneman, Ger J. M. Pruijn, Wendy Horstman, Walther J. van Venrooij, Reinhard Lührmann, and Nicholas J. Watkins.
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.
Journal of Biological Chemistry, 2002; 227; 48490-48500.



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.
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.
Nucleic Acids Research, 2000 15; 28; 3462-71.
Patrik Förch, Oscar Puig, Nancy Kedersha, Concepción Martínez, Sander Granneman, Bertrand Séraphin, Paul Anderson, and Juan Valcárcel.
The Apoptosis-Promoting Factor TIA-1 Is a Regulator of Alternative Pre-mRNA Splicing.
Molecular Cell, 2000; 6; 1089-1098.



Noor A. Eppens, Sietske Rensen, Sander Granneman, Hendrik A. Raue and Jaap Venema.
The roles of Rrp5p in the synthesis of yeast 18S and 5.8S rRNA can be functionally and physically separated.
RNA, 1999; 5; 779-93.