Emergence of the primordial pre-60S from the 90S pre-ribosome

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli

(2021) Philipp S. Erdmann et al.   Nature Communications

The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly

(2021) Gerald Ryan R. Aquino et al.   Nature Communications

Association of snR190 snoRNA chaperone with early pre-60S particles is regulated by the RNA helicase Dbp7 in yeast

(2021) Mariam Jaafar et al.   Nature Communications

Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1

(2020) Jasenko Zivanov et al.   IUCrJ

90S pre-ribosome transformation into the primordial 40S subunit

(2020) Jingdong Cheng et al.   SCIENCE

Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome

(2020) Benjamin Lau et al.   MOLECULAR CELL

Rrp5 Establishes a Checkpoint for 60S Assembly During 40S Maturation

(2019) Sohail Khoshnevis et al.   RNA

Conformational switches control early maturation of the eukaryotic small ribosomal subunit

(2019) Mirjam Hunziker et al.   eLife

Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration

(2019) Jingdong Cheng et al.   MOLECULAR CELL

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Modular assembly of the nucleolar pre-60S ribosomal subunit

(2018) Zahra Assur Sanghai et al.   NATURE

Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate

(2018) Dejian Zhou et al.   Protein & Cell

The Npa1p complex chaperones the assembly of the earliest eukaryotic large ribosomal subunit precursor

(2018) Clément Joret et al.   PLoS Genetics

Eurokaryotic Ribosome Assembly

(2018) Jochen Baßler et al.   Annual Review of Biochemistry

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

(2018) Jakob Trendel et al.   CELL

Suppressor mutations in Rpf2–Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation

(2018) Matthias Thoms et al.   Nature Communications

RNA helicases mediate structural transitions and compositional changes in pre-ribosomal complexes

(2018) Lukas Brüning et al.   Nature Communications

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1

(2017) Chengying Ma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome

(2017) Bebiana Sá-Moura et al.   PLoS One

Interaction network of the ribosome assembly machinery from a eukaryotic thermophile

(2017) Jochen Baßler et al.   PROTEIN SCIENCE

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1

(2017) Chengying Ma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular architecture of the 90S small subunit pre-ribosome

(2017) Qi Sun et al.   eLife

Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay

(2017) Jun Yang et al.   PLoS One

Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome

(2016) Markus Kornprobst et al.   CELL

Stepwise and dynamic assembly of the earliest precursors of small ribosomal subunits in yeast

(2016) Liman Zhang et al.   GENES & DEVELOPMENT

Gctf: Real-time CTF determination and correction

(2016) Kai Zhang   JOURNAL OF STRUCTURAL BIOLOGY

The complete chemical structure ofSaccharomyces cerevisiaerRNA: partial pseudouridylation of U2345 in 25S rRNA by snoRNA snR9

(2016) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

Disruption of ribosome assembly in yeast blocks cotranscriptional pre-rRNA processing and affects the global hierarchy of ribosome biogenesis

(2016) Jason Talkish et al.   RNA

Architecture of the yeast small subunit processome

(2016) Malik Chaker-Margot et al.   SCIENCE

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly

(2016) Mirjam Hunziker et al.   Nature Communications

The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins

(2015) Matthias Thoms et al.   CELL

Coordinated Ribosomal ITS2 RNA Processing by the Las1 Complex Integrating Endonuclease, Polynucleotide Kinase, and Exonuclease Activities

(2015) Lisa Gasse et al.   MOLECULAR CELL

Architecture of the Rix1–Rea1 checkpoint machinery during pre-60S-ribosome remodeling

(2015) Clara Barrio-Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Stage-specific assembly events of the 6-MDa small-subunit processome initiate eukaryotic ribosome biogenesis

(2015) Malik Chaker-Margot et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Architecture of the Rix1–Rea1 checkpoint machinery during pre-60S-ribosome remodeling

(2015) Clara Barrio-Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Stage-specific assembly events of the 6-MDa small-subunit processome initiate eukaryotic ribosome biogenesis

(2015) Malik Chaker-Margot et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains

(2014) M. Gamalinda et al.   GENES & DEVELOPMENT

Ribosome Assembly Factors Pwp1 and Nop12 Are Important for Folding of 5.8S rRNA during Ribosome Biogenesis in Saccharomyces cerevisiae

(2014) J. Talkish et al.   MOLECULAR AND CELLULAR BIOLOGY

Kinetic Analysis Demonstrates a Requirement for the Rat1 Exonuclease in Cotranscriptional Pre-rRNA Cleavage

(2014) Konstantin Axt et al.   PLoS One

Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases

(2014) Teresa Szczepińska et al.   PLoS Computational Biology

Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae

(2013) John L. Woolford et al.   GENETICS

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

(2013) Simon Lebaron et al.   MOLECULAR CELL

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

(2013) Yoshitaka Matsuo et al.   NATURE

Mak5 and Ebp2 Act Together on Early Pre-60S Particles and Their Reduced Functionality Bypasses the Requirement for the Essential Pre-60S Factor Nsa1

(2013) Dagmar Pratte et al.   PLoS One

A Translation-Like Cycle Is a Quality Control Checkpoint for Maturing 40S Ribosome Subunits

(2012) Bethany S. Strunk et al.   CELL

Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae

(2012) Thomas Hierlmeier et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Sander Granneman et al.   EMBO JOURNAL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA

(2011) Nicholas J. Watkins et al.   Wiley Interdisciplinary Reviews-RNA

Yeast Pre-rRNA Processing and Modification Occur Cotranscriptionally

(2010) Martin Koš et al.   MOLECULAR CELL

The AAA-ATPase Rea1 Drives Removal of Biogenesis Factors during Multiple Stages of 60S Ribosome Assembly

(2010) Jochen Baßler et al.   MOLECULAR CELL

The Bowen–Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Ψ1191 in yeast 18S rRNA

(2010) Britta Meyer et al.   NUCLEIC ACIDS RESEARCH

Mechanochemical Removal of Ribosome Biogenesis Factors from Nascent 60S Ribosomal Subunits

(2009) Cornelia Ulbrich et al.   CELL

RNA Helicase Prp43 and Its Co-factor Pfa1 Promote 20 to 18 S rRNA Processing Catalyzed by the Endonuclease Nob1

(2009) Brigitte Pertschy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Final Step in 5.8S rRNA Processing Is Cytoplasmic in Saccharomyces cerevisiae

(2009) E. Thomson et al.   MOLECULAR AND CELLULAR BIOLOGY

Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain

(2009) A. C. Lamanna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alopecia, Neurological Defects, and Endocrinopathy Syndrome Caused by Decreased Expression of RBM28, a Nucleolar Protein Associated with Ribosome Biogenesis

(2008) Janna Nousbeck et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Identification of pseudouridine methyltransferase in Escherichia coli

(2008) R. Ero et al.   RNA

YbeA is the m3  methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

(2008) E. Purta et al.   RNA