Translational control through ribosome heterogeneity and functional specialization

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide

(2021) Kathrin Leppek et al.   Cell Reports

rRNA expansion segment 27Lb modulates the factor recruitment capacity of the yeast ribosome and shapes the proteome

(2020) Vaishnavi Shankar et al.   NUCLEIC ACIDS RESEARCH

Monosomes actively translate synaptic mRNAs in neuronal processes

(2020) Anne Biever et al.   SCIENCE

In vitro ribosome synthesis and evolution through ribosome display

(2020) Michael J. Hammerling et al.   Nature Communications

MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments

(2020) Klemens Wild et al.   Nature Communications

Root of the Tree: The Significance, Evolution, and Origins of the Ribosome

(2020) Jessica C. Bowman et al.   CHEMICAL REVIEWS

Loss of m1acp3Ψ Ribosomal RNA Modification Is a Major Feature of Cancer

(2020) Artem Babaian et al.   Cell Reports

N6-adenosine methylation of ribosomal RNA affects lipid oxidation and stress resistance

(2020) Noa Liberman et al.   Science Advances

A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting

(2020) Racha Chouaib et al.   DEVELOPMENTAL CELL

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

(2020) Aldema Sas-Chen et al.   NATURE

H/ACA snoRNA levels are regulated during stem cell differentiation

(2020) Kathleen L McCann et al.   NUCLEIC ACIDS RESEARCH

Phenotypic effects of paralogous ribosomal proteins bL31A and bL31B in E. coli

(2020) Silva Lilleorg et al.   Scientific Reports

HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA

(2020) Virginie Marchand et al.   NUCLEIC ACIDS RESEARCH

The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2’-O-Me sites

(2020) Sowmya Ramachandran et al.   RNA

Ribosomopathies: New Therapeutic Perspectives

(2020) Emilien Orgebin et al.   Cells

Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit

(2020) Matthew L. Kraushar et al.   MOLECULAR CELL

Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments

(2020) Kathrin Leppek et al.   MOLECULAR CELL

Divergent rRNAs as regulators of gene expression at the ribosome level

(2019) Wooseok Song et al.   Nature Microbiology

Does Functional Specialization of Ribosomes Really Exist?

(2019) Max B Ferretti et al.   RNA

Local protein synthesis is a ubiquitous feature of neuronal pre- and postsynaptic compartments

(2019) Anne-Sophie Hafner et al.   SCIENCE

Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity

(2019) Ernest Mordret et al.   MOLECULAR CELL

Hallmarks of ribosomopathies

(2019) Kim R Kampen et al.   NUCLEIC ACIDS RESEARCH

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program

(2019) Maxime Janin et al.   ACTA NEUROPATHOLOGICA

Specialized eRpL22 paralogue-specific ribosomes regulate specific mRNA translation in spermatogenesis in Drosophila melanogaster

(2019) Catherine M. Mageeney et al.   MOLECULAR BIOLOGY OF THE CELL

Germline NPM1 mutations lead to altered rRNA 2′-O-methylation and cause dyskeratosis congenita

(2019) Daphna Nachmani et al.   NATURE GENETICS

Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing

(2019) Christel Enroth et al.   NUCLEIC ACIDS RESEARCH

Developmental changes of rRNA ribose methylations in the mouse

(2019) Jade Hebras et al.   RNA Biology

A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS

(2019) Mary McMahon et al.   eLife

Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth

(2019) Clemens Heissenberger et al.   NUCLEIC ACIDS RESEARCH

Invariable stoichiometry of ribosomal proteins in mouse brain tissues with aging

(2019) Susan Amirbeigiarab et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

The Expanding Riboverse

(2019) Sulima et al.   Cells

Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress

(2019) Mustafa Malik Ghulam et al.   NUCLEIC ACIDS RESEARCH

On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons

(2019) Toshiaki Shigeoka et al.   Cell Reports

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis

(2018) Rajiv K. Khajuria et al.   CELL

Ribosomes and cryo-EM: a duet

(2018) Alan Brown et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Heterogeneity and specialized functions of translation machinery: from genes to organisms

(2018) Naomi R. Genuth et al.   NATURE REVIEWS GENETICS

The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs

(2018) Michael S. Parker et al.   Frontiers in Genetics

Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression

(2018) Matthew M. Parks et al.   Science Advances

The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life

(2018) Naomi R. Genuth et al.   MOLECULAR CELL

Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis

(2018) Koshi Imami et al.   MOLECULAR CELL

Landscape of the complete RNA chemical modifications in the human 80S ribosome

(2018) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

Eurokaryotic Ribosome Assembly

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

Bacterial ribosome heterogeneity: Changes in ribosomal protein composition during transition into stationary growth phase

(2018) Silva Lilleorg et al.   BIOCHIMIE

Ribosome biogenesis factor Ltv1 chaperones the assembly of the small subunit head

(2018) Jason C. Collins et al.   JOURNAL OF CELL BIOLOGY

Sequencing-based methods for detection and quantitation of ribose methylations in RNA

(2018) Nicolai Krogh et al.   METHODS

Decoding the Function of Expansion Segments in Ribosomes

(2018) Kotaro Fujii et al.   MOLECULAR CELL

Ribosome–NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation

(2018) Alexandra G. Knorr et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype

(2018) Chad M. Kurylo et al.   Cell Reports

Ribosome Stoichiometry: From Form to Function

(2018) Edward Emmott et al.   TRENDS IN BIOCHEMICAL SCIENCES

Novel and known ribosomal causes of Diamond-Blackfan anaemia identified through comprehensive genomic characterisation

(2017) Lisa Mirabello et al.   JOURNAL OF MEDICAL GENETICS

Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide

(2017) Zhen Shi et al.   MOLECULAR CELL

Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements

(2017) Max B Ferretti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes

(2017) Jenny Erales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development

(2017) Mauro D. Locati et al.   RNA

Ribosomopathies: There’s strength in numbers

(2017) Eric W. Mills et al.   SCIENCE

Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements

(2017) Max B Ferretti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics

(2017) Tzu-Yu Liu et al.   Cell Systems

Characterizing RNA structures in vitro and in vivo with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2016) Kyle E. Watters et al.   METHODS

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

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

(2016) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

Profiling of 2′-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity

(2016) Nicolai Krogh et al.   NUCLEIC ACIDS RESEARCH

Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function

(2016) Katherine E. Sloan et al.   RNA Biology

Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity

(2016) Qais Al-Hadid et al.   RNA

Functional Dynamics within the Human Ribosome Regulate the Rate of Active Protein Synthesis

(2015) Angelica Ferguson et al.   MOLECULAR CELL

Structure of the human 80S ribosome

(2015) Heena Khatter et al.   NATURE

Differential Stoichiometry among Core Ribosomal Proteins

(2015) Nikolai Slavov et al.   Cell Reports

RiboVision suite for visualization and analysis of ribosomes

(2014) Chad R. Bernier et al.   FARADAY DISCUSSIONS

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

(2014) Shifeng Xue et al.   NATURE

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Secondary Structures of rRNAs from All Three Domains of Life

(2014) Anton S. Petrov et al.   PLoS One

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

Sudestada1, a Drosophila ribosomal prolyl-hydroxylase required for mRNA translation, cell homeostasis, and organ growth

(2014) M. J. Katz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OGFOD1 catalyzes prolyl hydroxylation of RPS23 and is involved in translation control and stress granule formation

(2014) R. S. Singleton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy

(2014) C. Loenarz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structures of the human and Drosophila 80S ribosome

(2013) Andreas M. Anger et al.   NATURE

Secondary structure and domain architecture of the 23S and 5S rRNAs

(2013) Anton S. Petrov et al.   NUCLEIC ACIDS RESEARCH

An evolutionary conserved pattern of 18S rRNA sequence complementarity to mRNA 5′ UTRs and its implications for eukaryotic gene translation regulation

(2013) Josef Pánek et al.   NUCLEIC ACIDS RESEARCH

Specialized Yeast Ribosomes: A Customized Tool for Selective mRNA Translation

(2013) Johann W. Bauer et al.   PLoS One

Ribosomal deficiencies in Diamond-Blackfan anemia impair translation of transcripts essential for differentiation of murine and human erythroblasts

(2011) R. Horos et al.   BLOOD

Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning

(2011) Nadya Kondrashov et al.   CELL

rRNA Pseudouridylation Defects Affect Ribosomal Ligand Binding and Translational Fidelity from Yeast to Human Cells

(2011) Karen Jack et al.   MOLECULAR CELL

An efficient factor-depleted mammalian in vitro translation system

(2011) Aurélie M Rakotondrafara et al.   Nature Protocols

Diagnostic and prognostic signatures from the small non-coding RNA transcriptome in prostate cancer

(2011) E S Martens-Uzunova et al.   ONCOGENE

Nol9 is a novel polynucleotide 5′-kinase involved in ribosomal RNA processing

(2010) Katrin Heindl et al.   EMBO JOURNAL

The ribosomal basis of diamond-blackfan anemia: mutation and database update

(2010) Ilenia Boria et al.   HUMAN MUTATION

Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome

(2010) Johannes G Dauwerse et al.   NATURE GENETICS

Expression of ribosomal protein L22e family members in Drosophila melanogaster: rpL22-like is differentially expressed and alternatively spliced

(2010) M. G. Kearse et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution

(2010) J.-P. Armache et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Severe Zinc Depletion ofEscherichia coli

(2009) Alison I. Graham et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ribosome reactivation by replacement of damaged proteins

(2009) Arto Pulk et al.   MOLECULAR MICROBIOLOGY

Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping

(2008) J. Esguerra et al.   RNA