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

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

(2016) Markus Kornprobst et al.   CELL

Emerging roles of RNA modifications in bacteria

(2016) Carmelita Nora Marbaniang et al.   CURRENT OPINION IN MICROBIOLOGY

Effects of the Bowen-Conradi syndrome mutation in EMG1 on its nuclear import, stability and nucleolar recruitment

(2016) Ahmed S. Warda et al.   HUMAN MOLECULAR GENETICS

NML-mediated rRNA base methylation links ribosomal subunit formation to cell proliferation in a p53-dependent manner

(2016) Tsuyoshi Waku et al.   JOURNAL OF CELL SCIENCE

Pathways to Specialized Ribosomes: The Brussels Lecture

(2016) Jonathan D. Dinman   JOURNAL OF MOLECULAR BIOLOGY

Nucleocytoplasmic Transport of RNAs and RNA–Protein Complexes

(2016) Katherine E. Sloan et al.   JOURNAL OF MOLECULAR BIOLOGY

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

Unusual C′/D′ motifs enable box C/D snoRNPs to modify multiple sites in the same rRNA target region

(2016) Robert Willem van Nues et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

High-throughput single-base resolution mapping of RNA 2΄-O-methylated residues

(2016) Danny Incarnato et al.   NUCLEIC ACIDS RESEARCH

Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA

(2016) Virginie Marchand 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

An updated human snoRNAome

(2016) Hadi Jorjani et al.   NUCLEIC ACIDS RESEARCH

Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans

(2016) Britta Meyer et al.   NUCLEIC ACIDS RESEARCH

Box C/D guide RNAs recognize a maximum of 10 nt of substrates

(2016) Zuxiao Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing

(2016) Marina Falaleeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

Functions of Ribosomal Proteins in Assembly of Eukaryotic Ribosomes In Vivo

(2015) Jesús de la Cruz et al.   Annual Review of Biochemistry

Translating the Genome in Time and Space: Specialized Ribosomes, RNA Regulons, and RNA-Binding Proteins

(2015) Zhen Shi et al.   Annual Review of Cell and Developmental Biology

Structural Snapshots of Actively Translating Human Ribosomes

(2015) Elmar Behrmann et al.   CELL

The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis

(2015) Christiane Zorbas et al.   MOLECULAR BIOLOGY OF THE CELL

Structure of the human 80S ribosome

(2015) Heena Khatter et al.   NATURE

Noncoding RNAs in eukaryotic ribosome biogenesis and function

(2015) Denis L J Lafontaine   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of a new ribose methylation in the 18S rRNA of S. cerevisiae

(2015) Jun Yang et al.   NUCLEIC ACIDS RESEARCH

Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1

(2015) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

‘View From A Bridge’: A New Perspective on Eukaryotic rRNA Base Modification

(2015) Sunny Sharma et al.   TRENDS IN BIOCHEMICAL SCIENCES

Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan

(2015) Markus Schosserer et al.   Nature Communications

Noncoding RNAs in eukaryotic ribosome biogenesis and function

(2015) Denis L J Lafontaine   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120

(2015) Gabrielle Bourgeois et al.   PLoS One

RNA-guided isomerization of uridine to pseudouridine—pseudouridylation

(2015) Yi-Tao Yu et al.   RNA Biology

Profiling of Ribose Methylations in RNA by High-Throughput Sequencing

(2014) Ulf Birkedal et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

Assembly and nuclear export of pre-ribosomal particles in budding yeast

(2014) Stefan Gerhardy et al.   CHROMOSOMA

Human NAT10 Is an ATP-dependent RNA Acetyltransferase Responsible forN4-Acetylcytidine Formation in 18 S Ribosomal RNA (rRNA)

(2014) Satoshi Ito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Physical and Functional Interaction between the Methyltransferase Bud23 and the Essential DEAH-Box RNA Helicase Ecm16

(2014) R. Sardana et al.   MOLECULAR AND CELLULAR BIOLOGY

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

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

(2014) Ralph D. Hector et al.   NUCLEIC ACIDS RESEARCH

The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21

(2014) Katherine E. Sloan et al.   NUCLEIC ACIDS RESEARCH

Partial Methylation at Am100 in 18S rRNA of Baker's Yeast Reveals Ribosome Heterogeneity on the Level of Eukaryotic rRNA Modification

(2014) Markus Buchhaupt et al.   PLoS One

Structural and functional studies of Bud23–Trm112 reveal 18S rRNAN7-G1575 methylation occurs on late 40S precursor ribosomes

(2014) Juliette Létoquart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the ribosome at atomic resolution

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

A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase

(2014) Roman Martin et al.   RNA

WBSCR22/Merm1 is required for late nuclear pre-ribosomal RNA processing and mediates N7-methylation of G1639 in human 18S rRNA

(2014) Sara Haag et al.   RNA

A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability

(2014) Andriana Gigova et al.   RNA

Hepatic rRNA Transcription Regulates High-Fat-Diet-Induced Obesity

(2014) Shohei Oie et al.   Cell Reports

An overview of pre-ribosomal RNA processing in eukaryotes

(2014) Anthony K. Henras et al.   Wiley Interdisciplinary Reviews-RNA

Activation of the tumor suppressor p53 upon impairment of ribosome biogenesis

(2013) Sladana Bursac et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

p53 Acts as a Safeguard of Translational Control by Regulating Fibrillarin and rRNA Methylation in Cancer

(2013) Virginie Marcel et al.   CANCER CELL

Beyond microRNA – Novel RNAs derived from small non-coding RNA and their implication in cancer

(2013) Elena S. Martens-Uzunova et al.   CANCER LETTERS

Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae

(2013) John L. Woolford et al.   GENETICS

Eukaryotic ribosome biogenesis at a glance

(2013) E. Thomson et al.   JOURNAL OF CELL SCIENCE

The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors

(2013) Lionel Tafforeau et al.   MOLECULAR CELL

Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae

(2013) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively

(2013) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

Identification of novel methyltransferases, Bmt5 and Bmt6, responsible for the m3U methylations of 25S rRNA in Saccharomyces cerevisiae

(2013) S. Sharma et al.   NUCLEIC ACIDS RESEARCH

The evolution of the ribosome biogenesis pathway from a yeast perspective

(2013) Ingo Ebersberger et al.   NUCLEIC ACIDS RESEARCH

Dyskerin depletion increases VEGF mRNA internal ribosome entry site-mediated translation

(2013) Laura Rocchi et al.   NUCLEIC ACIDS RESEARCH

Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly

(2013) Benjamin Rothé et al.   NUCLEIC ACIDS RESEARCH

Burkitt’s lymphoma-associated c-Myc mutations converge on a dramatically altered target gene response and implicate Nol5a/Nop56 in oncogenesis

(2013) V H Cowling et al.   ONCOGENE

Elevated snoRNA biogenesis is essential in breast cancer

(2013) H Su et al.   ONCOGENE

H/ACA Small RNA Dysfunctions in Disease Reveal Key Roles for Noncoding RNA Modifications in Hematopoietic Stem Cell Differentiation

(2013) Cristian Bellodi et al.   Cell Reports

The 5S RNP Couples p53 Homeostasis to Ribosome Biogenesis and Nucleolar Stress

(2013) Katherine E. Sloan et al.   Cell Reports

Small nucleolar RNAs in cancer

(2012) Kaiissar Mannoor et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Trm112 Is Required for Bud23-Mediated Methylation of the 18S rRNA at Position G1575

(2012) S. Figaro et al.   MOLECULAR AND CELLULAR BIOLOGY

Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin

(2012) Thomas Schubert et al.   MOLECULAR CELL

Specialized ribosomes: a new frontier in gene regulation and organismal biology

(2012) Shifeng Xue et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA

(2012) Christian Peifer et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

Mutual protection of ribosomal proteins L5 and L11 from degradation is essential for p53 activation upon ribosomal biogenesis stress

(2012) S. Bursac et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transfer RNA modifications: nature's combinatorial chemistry playground

(2012) Jane E. Jackman et al.   Wiley Interdisciplinary Reviews-RNA

The small-nucleolar RNAs commonly used for microRNA normalisation correlate with tumour pathology and prognosis

(2011) H E Gee et al.   BRITISH JOURNAL OF CANCER

The cancerous translation apparatus

(2011) Craig R Stumpf et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2011) Robert Willem van Nues et al.   EMBO JOURNAL

Requirement of rRNA Methylation for 80S Ribosome Assembly on a Cohort of Cellular Internal Ribosome Entry Sites

(2011) A. Basu et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2011) Karen Jack et al.   MOLECULAR CELL

Structural basis for site-specific ribose methylation by box C/D RNA protein complexes

(2011) Jinzhong Lin et al.   NATURE

A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly

(2011) Dragomir B. Krastev et al.   NATURE CELL BIOLOGY

Loss of ribosomal RNA modification causes developmental defects in zebrafish

(2011) Sayomi Higa-Nakamine et al.   NUCLEIC ACIDS RESEARCH

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

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates

(2011) B. S. Strunk et al.   SCIENCE

The Structure of the Eukaryotic Ribosome at 3.0 A Resolution

(2011) A. Ben-Shem et al.   SCIENCE

Functional specialization of ribosomes?

(2011) Wendy V. Gilbert   TRENDS IN BIOCHEMICAL SCIENCES

RNA nucleotide methylation

(2011) Yuri Motorin et al.   Wiley Interdisciplinary Reviews-RNA

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

PLEXY: efficient target prediction for box C/D snoRNAs

(2010) Stephanie Kehr et al.   BIOINFORMATICS

Loss of Function of the Tumor Suppressor DKC1 Perturbs p27 Translation Control and Contributes to Pituitary Tumorigenesis

(2010) C. Bellodi et al.   CANCER RESEARCH

U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP

(2010) Guowei Wu et al.   EMBO JOURNAL

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

(2010) Sander Granneman et al.   EMBO JOURNAL

Deregulation of oncogene-induced senescence and p53 translational control in X-linked dyskeratosis congenita

(2010) Cristian Bellodi et al.   EMBO JOURNAL

When ribosomes go bad: diseases of ribosome biogenesis

(2010) Emily F. Freed et al.   Molecular BioSystems

Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer

(2010) Jipei Liao et al.   Molecular Cancer

Yeast Pre-rRNA Processing and Modification Occur Cotranscriptionally

(2010) Martin Koš et al.   MOLECULAR CELL

The ribosome assembly factor Nep1 responsible for Bowen–Conradi syndrome is a pseudouridine-N1-specific methyltransferase

(2010) Jan Philip Wurm et al.   NUCLEIC ACIDS RESEARCH

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

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

Mutation of a Gene Essential for Ribosome Biogenesis, EMG1, Causes Bowen-Conradi Syndrome

(2009) Joy Armistead et al.   AMERICAN JOURNAL OF HUMAN GENETICS

RNAsnoop: efficient target prediction for H/ACA snoRNAs

(2009) Hakim Tafer et al.   BIOINFORMATICS

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

(2009) Markus T. Bohnsack et al.   MOLECULAR CELL

Structural Mechanism of Substrate RNA Recruitment in H/ACA RNA-Guided Pseudouridine Synthase

(2009) Jingqi Duan et al.   MOLECULAR CELL

Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy

(2009) Agnès Baudin-Baillieu et al.   NUCLEIC ACIDS RESEARCH

Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing

(2009) X.-h. Liang et al.   RNA

Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

(2008) W. A. Decatur et al.   MOLECULAR AND CELLULAR BIOLOGY

Bud23 Methylates G1575 of 18S rRNA and Is Required for Efficient Nuclear Export of Pre-40S Subunits

(2008) J. White et al.   MOLECULAR AND CELLULAR BIOLOGY

The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site

(2008) A. B. Taylor et al.   NUCLEIC ACIDS RESEARCH

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

(2008) J. Esguerra et al.   RNA