List of works - Sander Granneman

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

scientific article

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

scientific article

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

scientific article

Building ribosomes: even more expensive than expected?

scientific article published in June 2007

Cell populations can use aneuploidy to survive telomerase insufficiency

scientific article published on 22 October 2015

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 7 May 2010

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

scientific article

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

scientific article

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

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

scientific article published on 01 May 2020

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

scientific article published on 28 September 2017

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

scientific article

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

scientific article

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

scholarly article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Probing the yeast proteome for RNA-processing factors

scientific article

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

scientific article

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

scientific article

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

scientific article published on 01 March 2019

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

scientific article

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

scientific article published on 10 October 2017

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

scientific article

Ribosome biogenesis: of knobs and RNA processing

scientific article published on May 2004

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

scientific article published on 7 October 2014

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

scientific article published on 7 November 2016

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

scientific article

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

scientific article

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

scientific article published on 8 September 2014

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

scientific article

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

scientific article

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

scientific article published on 24 February 2015

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

scientific article

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

scientific article published on 24 May 2022

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 12 October 2020

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

scientific article

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

scholarly article by Wiebke Wlotzka published in July 2011

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

scientific article

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

scientific article

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

scientific article published on June 1999

The small-subunit processome is a ribosome assembly intermediate

scientific article

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

scientific article published on 17 December 2015

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

scientific article published on 27 May 2021

List of works by Sander Granneman

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

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

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

Building ribosomes: even more expensive than expected?

Cell populations can use aneuploidy to survive telomerase insufficiency

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Probing the yeast proteome for RNA-processing factors

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

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

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

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

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

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

Ribosome biogenesis: of knobs and RNA processing

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

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

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

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

The small-subunit processome is a ribosome assembly intermediate

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

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