S. Granneman

发表

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

David Tollervey, Sander Granneman, D. Tollervey, 2011, Proceedings of the National Academy of Sciences.

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

Guido Sanguinetti, Alina Selega, Christel Sirocchi, 2016, Nature Methods.

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation

R. V. van Nues, J. Tree, G. Viero, 2020, eLife.

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

M. Selbach, B. Beckmann, U. Ohler, 2018, Nature Communications.

Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction

M. Selbach, B. Beckmann, U. Ohler, 2018, bioRxiv.

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

E. Petfalski, D. Tollervey, J. Rappsilber, 2014, Nucleic acids research.

JCB_201408111 1..18

Sarah A. Clark, D. Tollervey, E. Hurt, 2015 .

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

Sarah A. Clark, D. Tollervey, E. Hurt, 2015, The Journal of cell biology.

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

D. Tollervey, Grzegorz Kudla, R. V. van Nues, 2011, The EMBO journal.

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

G. Pruijn, J. Gallagher, S. Baserga, 2003, Nucleic acids research.

ERS 1 a seven transmembrane domain protein from Saccharomyces cerevisiae

G. Pruijn, J. Gallagher, S. Baserga, 2003 .

The human Imp 3 and Imp 4 proteins form a ternary complex with hMpp 10 , which only interacts with the U 3 snoRNA in 60 ± 80 S ribonucleoprotein complexes

G. Pruijn, J. Gallagher, S. Baserga, 2022 .

Hfq CLASH uncovers sRNA-target interaction networks enhancing adaptation to nutrient availability

R. V. van Nues, J. Tree, G. Viero, 2018, bioRxiv.

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

S. Cockroft, M. Oeffinger, C. Trahan, 2017, Nature Communications.

RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression

Grzegorz Kudla, Ronan K. Carroll, P. Arede, 2022, Nature Communications.

The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins

B. Beckmann, A. von Kriegsheim, P. Arede, 2022, Nature Communications.

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 *

G. Pruijn, R. Lührmann, W. V. van Venrooij, 2002, The Journal of Biological Chemistry.

Edinburgh Research Explorer Identification of bacteriophage-encoded anti-sRNAs in pathogenic escherichia coli

D. Tollervey, J. Tree, S. McAteer, 2014 .

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

Sarah A. Clark, D. Tollervey, E. Hurt, 2014, The Journal of cell biology.

Proof Only Proof Only The Nrd 1-like protein Seb 1 coordinates cotranscriptional 3 ′ end processing and polyadenylation site selection

J. Bähler, S. Marguerat, B. Tian, 2016 .

Building Ribosomes: Even More Expensive Than Expected?

D. Tollervey, S. Granneman, 2007, Current Biology.

Publisher Correction: RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance

M. Wilkins, J. Tree, C. Pang, 2022, Nature Communications.

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.

H. Pluk, R. Terns, M. Terns, 2000, Nucleic acids research.

Temporal-iCLIP captures co-transcriptional RNA-protein interactions

Torben Heick Jensen, S. Granneman, Rune Thomsen, 2023, Nature Communications.

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

L. Vasiljeva, S. Granneman, Cornelia Kilchert, 2013, Genes & development.

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

Guido Sanguinetti, Gabriele Schweikert, Alina Selega, 2017, Nature Communications.

Cell populations can use aneuploidy to survive telomerase insufficiency

T. Le Bihan, S. Granneman, C. Millet, 2015, Nature Communications.

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

K. Entian, P. Kötter, D. Lafontaine, 2017, PLoS genetics.

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

Juri Rappsilber, Maryia Trubitsyna, Sander Granneman, 2017, bioRxiv.

The apoptosis-promoting factor TIA-1 is a regulator of alternative pre-mRNA splicing.

J. Valcárcel, B. Séraphin, P. Anderson, 2000, Molecular cell.

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

S. Baserga, S. Granneman, 2005, Current opinion in cell biology.

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

J. Gallagher, S. Baserga, Y. Osheim, 2004, Genes & development.

Ribosome biogenesis: of knobs and RNA processing.

Sander Granneman, S. Baserga, S. Granneman, 2004, Experimental cell research.

Rrp5 Binding at Multiple Sites Coordinates Pre-rRNA Processing and Assembly

D. Tollervey, Å. Segerstolpe, J. Rappsilber, 2013, Molecular cell.

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

D. Tollervey, B. Böttcher, R. V. van Nues, 2012, Nature Structural &Molecular Biology.

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

D. Tollervey, Grzegorz Kudla, Wiebke Wlotzka, 2011 .

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

D. Tollervey, Grzegorz Kudla, Wiebke Wlotzka, 2011, The EMBO journal.

The Putative NTPase Fap7 Mediates Cytoplasmic 20S Pre-rRNA Processing through a Direct Interaction with Rps14

S. Baserga, M. R. Nandineni, S. Granneman, 2005, Molecular and Cellular Biology.

The Putative NTPase Fap 7 Mediates Cytoplasmic 20 S Pre-rRNA Processing through a Direct Interaction with Rps 14 †

S. Baserga, M. R. Nandineni, S. Granneman, 2005 .

Prp43 Bound at Different Sites on the Pre-rRNA Performs Distinct Functions in Ribosome Synthesis

David Tollervey, Roman Martin, Enrico Schleiff, 2009, Molecular cell.

Edinburgh Research Explorer Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli

David Tollervey, Sander Granneman, D. Tollervey, 2022 .

Puf6 primes 60S pre-ribosome nuclear export at low temperature

Ludovic C. Gillet, V. G. Panse, R. Aebersold, 2021, Nature Communications.

The Small-Subunit Processome Is a Ribosome Assembly Intermediate

J. Gallagher, S. Baserga, Kara A. Bernstein, 2004, Eukaryotic Cell.

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

David Tollervey, Sander Granneman, E. Petfalski, 2009, Proceedings of the National Academy of Sciences.

Fine-tuning of RecBCD expression by post-transcriptional regulation is required for optimal DNA repair in Escherichia coli

M. Karoui, S. Granneman, I. Iosub, 2021, bioRxiv.

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

Stuart Aitken, Thierry Le Bihan, Sander Granneman, 2014, Nucleic acids research.

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

E. Petfalski, D. Tollervey, Agata Swiatkowska, 2010, The EMBO journal.

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

M. Selbach, B. Beckmann, U. Ohler, 2018, bioRxiv.

The role of RNA‐binding proteins in mediating adaptive responses in Gram‐positive bacteria

S. Granneman, Niki Christopoulou, 2021, The FEBS journal.

The DEAH-box Helicase Dhr1 Dissociates U3 from the Pre-rRNA to Promote Formation of the Central Pseudoknot

Arlen W. Johnson, E. Marcotte, D. Tollervey, 2015, PLoS biology.

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

D. Tollervey, E. Hurt, S. Granneman, 2013, Nature.

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

D. Tollervey, B. Böttcher, E. Hurt, 2012, Nature Structural &Molecular Biology.

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

E. Petfalski, D. Tollervey, S. Granneman, 2011, The EMBO journal.

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

J. Venema, S. Granneman, N. A. Eppens, 1999, RNA.

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

D. Tollervey, Å. Segerstolpe, J. Rappsilber, 2012, Nucleic acids research.

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

S. Baserga, Y. Osheim, A. Beyer, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Comprehensive Mutational Analysis of Yeast DEXD/H Box RNA Helicases Involved in Large Ribosomal Subunit Biogenesis

S. Baserga, Kara A. Bernstein, S. Granneman, 2006, Molecular and Cellular Biology.

Role of Pre-rRNA Base Pairing and 80S Complex Formation in Subnucleolar Localization of the U3 snoRNP

G. Pruijn, R. Lührmann, W. V. van Venrooij, 2004, Molecular and Cellular Biology.

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

L. Steinmetz, D. Tollervey, C. Guthrie, 2015, PLoS genetics.

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

B. Beckmann, S. Granneman, 2019, Methods in molecular biology.

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

J. Bähler, S. Marguerat, B. Tian, 2016, Genes & development.

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

G. Sanguinetti, J. Beggs, Yuanhua Huang, 2015, Genome Biology.

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

Grzegorz Kudla, Shaun Webb, S. Granneman, 2014, Genome Biology.

Nrd 1-Nab 3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast

Grzegorz Kudla, Shaun Webb, S. Granneman, 2013 .

Monitoring Protein-RNA Interaction Dynamics in vivo at High Temporal Resolution using χCRAC.

T. Jensen, R. V. van Nues, S. Granneman, 2020, Journal of visualized experiments : JoVE.

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

L. Vasiljeva, S. Granneman, Sneha Shah, 2015, Cell reports.

Probing the yeast proteome for RNA-processing factors

S. Baserga, S. Granneman, 2003, Genome Biology.

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

D. Tollervey, M. Bohnsack, S. Granneman, 2012, Methods in enzymology.

diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data

Ka Ying Toby Law, G. Sanguinetti, S. Granneman, 2021, Genome Biology.

Differential BUM-HMM: a robust statistical modelling approach for detecting RNA flexibility changes in high-throughput structure probing data

Guido Sanguinetti, Paolo Marangio, Sander Granneman, 2020, bioRxiv.

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

S. Belikov, S. Granneman, L. Wieslander, 2018, Nucleic acids research.

Comprehensive Mutational Analysis of Yeast DEXD/H Box RNA Helicases Required for Small Ribosomal Subunit Synthesis

S. Baserga, Kara A. Bernstein, F. Bleichert, 2006, Molecular and Cellular Biology.

The mRNA derived MalH sRNA contributes to alternative carbon source utilization by tuning maltoporin expression in E. coli

R. V. van Nues, G. Viero, M. Marchioretto, 2020, RNA biology.

Advantages and limitations of UV cross‐linking analysis of protein–RNA interactomes in microbes

S. Granneman, H. Mccaughan, Sofia Esteban-Serna, 2023, Molecular microbiology.

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

D. Tollervey, J. Tree, S. McAteer, 2018, Nucleic acids research.

RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance

M. Wilkins, J. Tree, C. Pang, 2022, Nature Communications.

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

D. Tollervey, J. Wong, J. Tree, 2018, Methods in molecular biology.

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

S. Baserga, M. R. Nandineni, S. Granneman, 2006, Nucleic acids research.

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

G. Sanguinetti, J. Beggs, Yuanhua Huang, 2015, Genome Biology.

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

D. Tollervey, J. Tree, S. McAteer, 2014 .

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

D. Tollervey, J. Tree, S. McAteer, 2014 .

Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen

J. Penadés, A. Haag, S. Granneman, 2021, PLoS pathogens.

Massive genome decay and insertion sequence expansion drive the evolution of a novel host-restricted bacterial pathogen

J. Penadés, A. Haag, S. Granneman, 2020 .

pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data

S. Granneman, Niki Christopoulou, Salomé Brunon, 2024, Life science alliance.

pyRBDome: A comprehensive computational platform for enhancing and interpreting RNA-binding proteome data

S. Granneman, Niki Christopoulou, Salomé Brunon, 2023, bioRxiv.