Functional implications of ribosomal RNA methylation in response to environmental stress

Molecular functions of small regulatory noncoding RNA

(2013) Yong Huang et al.   BIOCHEMISTRY-MOSCOW

RNA decay via 3′ uridylation

(2013) Daniel D. Scott et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

The ribosome as a versatile catalyst: reactions at the peptidyl transferase center

(2013) Marina V Rodnina   CURRENT OPINION IN STRUCTURAL BIOLOGY

Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing

(2013) Dan Dominissini et al.   Nature Protocols

RNA pseudouridylation: new insights into an old modification

(2013) Junhui Ge et al.   TRENDS IN BIOCHEMICAL SCIENCES

N6-methyl-adenosine modification in messenger and long non-coding RNA

(2013) Tao Pan   TRENDS IN BIOCHEMICAL SCIENCES

FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA

(2013) Ye Fu et al.   Nature Communications

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs

(2013) Sarit Edelheit et al.   PLoS Genetics

Mapping and significance of the mRNA methylome

(2013) Tennille Sibbritt et al.   Wiley Interdisciplinary Reviews-RNA

Mutations in NSUN2 Cause Autosomal- Recessive Intellectual Disability

(2012) Lia Abbasi-Moheb et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Structure and Function of Noncanonical Nucleobases

(2012) Thomas Carell et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs

(2012) Basma El Yacoubi et al.   Annual Review of Genetics

Mechanisms of SecM-Mediated Stalling in the Ribosome

(2012) James Gumbart et al.   BIOPHYSICAL JOURNAL

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Regulation of small RNA stability: methylation and beyond

(2012) Lijuan Ji et al.   CELL RESEARCH

Structural Insights into Methyltransferase KsgA Function in 30S Ribosomal Subunit Biogenesis

(2012) Daniel Boehringer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mass spectrometry in the biology of RNA and its modifications

(2012) Anders M.B. Giessing et al.   Journal of Proteomics

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Mapping recently identified nucleotide variants in the genome and transcriptome

(2012) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity

(2012) Satoshi Kimura et al.   NUCLEIC ACIDS RESEARCH

Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m 7 G2069 and m 2 G2445 modifications in Escherichia coli 23S rRNA

(2012) Kai-Tuo Wang et al.   NUCLEIC ACIDS RESEARCH

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

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

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

The last rRNA methyltransferase of E. coli revealed: The yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA

(2012) A. Y. Golovina et al.   RNA

The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy

(2012) A. Benitez-Paez et al.   RNA

Reversible RNA adenosine methylation in biological regulation

(2012) Guifang Jia et al.   TRENDS IN GENETICS

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

(2012) Yoichiro Sugimoto et al.   GENOME BIOLOGY

N6-methyl-adenosine (m6A) in RNA: An Old Modification with A Novel Epigenetic Function

(2012) Yamei Niu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Transforming biochemical engineering with cell-free biology

(2011) James R. Swartz   AICHE JOURNAL

Human Mitochondrial tRNAs: Biogenesis, Function, Structural Aspects, and Diseases

(2011) Tsutomu Suzuki et al.   Annual Review of Genetics

Methylated 23S rRNA nucleotide m2G1835 of Escherichia coli ribosome facilitates subunit association

(2011) Ilya A. Osterman et al.   BIOCHIMIE

Biosynthesis and function of tRNA modifications in Archaea

(2011) Gabriela Phillips et al.   CURRENT OPINION IN MICROBIOLOGY

Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

(2011) Lore Cloots et al.   CURRENT OPINION IN MICROBIOLOGY

Ribosome evolution: Emergence of peptide synthesis machinery

(2011) Koji Tamura   JOURNAL OF BIOSCIENCES

Complete Modification Maps for the Cytosolic Small and Large Subunit rRNAs of Euglena gracilis: Functional and Evolutionary Implications of Contrasting Patterns between the Two rRNA Components

(2011) Murray N. Schnare et al.   JOURNAL OF MOLECULAR BIOLOGY

YhiQ Is RsmJ, the Methyltransferase Responsible for Methylation of G1516 in 16S rRNA of E. coli

(2011) Georgeta N. Basturea et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Bacterial transcriptomics: what is beyond the RNA horiz-ome?

(2011) Marc Güell et al.   NATURE REVIEWS MICROBIOLOGY

RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift

(2011) F. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology ofHaloferax volcanii

(2011) Jörg Soppa   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

RNA nucleotide methylation

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

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

S-Adenosylmethionine-dependent radical-based modification of biological macromolecules

(2010) Mohamed Atta et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

RlmN and Cfr are Radical SAM Enzymes Involved in Methylation of Ribosomal RNA

(2010) Feng Yan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Metabolomic and transcriptomic stress response of Escherichia coli

(2010) Szymon Jozefczuk et al.   Molecular Systems Biology

Grand Challenge Commentary: RNA epigenetics?

(2010) Chuan He   Nature Chemical Biology

The RNA modification database, RNAMDB: 2011 update

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

Detection of RNA modifications

(2010) Stefanie Kellner et al.   RNA Biology

Subribosomal particle analysis reveals the stages of bacterial ribosome assembly at which rRNA nucleotides are modified

(2010) T. Siibak et al.   RNA

Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD

(2010) R. Ero et al.   RNA

Parallel Isotope-Based Quantification of Modified tRNA Nucleosides

(2009) Tobias Brückl et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes

(2009) Henri Grosjean et al.   FEBS LETTERS

Next generation sequencing of microbial transcriptomes: challenges and opportunities

(2009) Arnoud H.M. van Vliet   FEMS MICROBIOLOGY LETTERS

Structural and Functional Divergence within the Dim1/KsgA Family of rRNA Methyltransferases

(2009) Nagesh Pulicherla et al.   JOURNAL OF MOLECULAR BIOLOGY

Integrating multiple 'omics' analysis for microbial biology: application and methodologies

(2009) W. Zhang et al.   MICROBIOLOGY-SGM

YgdE is the 2′-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA

(2009) Elzbieta Purta et al.   MOLECULAR MICROBIOLOGY

Impact of rRNA methylations on ribosome recycling and fidelity of initiation inEscherichia coli

(2009) Anuradha Seshadri et al.   MOLECULAR MICROBIOLOGY

Single 23S rRNA mutations at the ribosomal peptidyl transferase centre confer resistance to valnemulin and other antibiotics inMycobacterium smegmatisby perturbation of the drug binding pocket

(2009) Katherine S. Long et al.   MOLECULAR MICROBIOLOGY

Tertiary interactions within the ribosomal exit tunnel

(2009) Andrey Kosolapov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA

(2009) Satoshi Kimura et al.   NUCLEIC ACIDS RESEARCH

5-methylcytosine in RNA: detection, enzymatic formation and biological functions

(2009) Yuri Motorin et al.   NUCLEIC ACIDS RESEARCH

Proteome changes in human bronchoalveolar cells following styrene exposure indicate involvement of oxidative stress in the molecular-response mechanism

(2009) Nora Mörbt et al.   PROTEOMICS

Interplay between the heat shock response and translation in Escherichia coli

(2009) Aviram Rasouly et al.   RESEARCH IN MICROBIOLOGY

Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria

(2009) A. M. B. Giessing et al.   RNA

2'-O-methylation stabilizes Piwi-associated small RNAs and ensures DNA elimination in Tetrahymena

(2009) H. M. Kurth et al.   RNA

Path of Nascent Polypeptide in Exit Tunnel Revealed by Molecular Dynamics Simulation of Ribosome

(2008) Hisashi Ishida et al.   BIOPHYSICAL JOURNAL

RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

(2008) Henri Grosjean et al.   BMC GENOMICS

Structure, dynamics, and function of RNA modification enzymes

(2008) Ryuichiro Ishitani et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

YccW is the m5C Methyltransferase Specific for 23S rRNA Nucleotide 1962

(2008) Elzbieta Purta et al.   JOURNAL OF MOLECULAR BIOLOGY

Ribosome biogenesis; the KsgA protein throws a methyl-mediated switch in ribosome assembly

(2008) Chand S. Mangat et al.   MOLECULAR MICROBIOLOGY

Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA

(2008) Keith Connolly et al.   MOLECULAR MICROBIOLOGY

Small non-coding RNAs in animal development

(2008) Giovanni Stefani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A conserved rRNA methyltransferase regulates ribosome biogenesis

(2008) Zhili Xu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA cytosine methylation analysis by bisulfite sequencing

(2008) M. Schaefer et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2008 update

(2008) A. Czerwoniec et al.   NUCLEIC ACIDS RESEARCH

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

The ybiN Gene of Escherichia coli Encodes Adenine-N6 Methyltransferase Specific for Modification of A1618 of 23 S Ribosomal RNA, a Methylated Residue Located Close to the Ribosomal Exit Tunnel

(2007) Petr V. Sergiev et al.   JOURNAL OF MOLECULAR BIOLOGY