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RNA nucleotide methylation

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Abstract Methylation of RNA occurs at a variety of atoms, nucleotides, sequences and tertiary structures. Strongly related to other posttranscriptional modifications, methylation of different RNA species includes tRNA, rRNA, mRNA, tmRNA, snRNA, snoRNA, miRNA, and viral RNA. Different catalytic strategies are employed for RNA methylation by a variety of RNA‐methyltransferases which fall into four superfamilies. This review outlines the different functions of methyl groups in RNA, including biophysical, biochemical and metabolic stabilization of RNA, quality control, resistance to antibiotics, mRNA reading frame maintenance, deciphering of normal and altered genetic code, selenocysteine incorporation, tRNA aminoacylation, ribotoxins, splicing, intracellular trafficking, immune response, and others. Connections to other fields including gene regulation, DNA repair, stress response, and possibly histone acetylation and exocytosis are pointed out. WIREs RNA 2011 2 611–631 DOI: 10.1002/wrna.79 This article is categorized under: RNA Processing > RNA Editing and Modification

Diversity of nucleotide methylation. (a) Methylation sites on the chemical structures of the four major ribonucleotides, inosine, and pseudouridine.3,4 Note that multiple modifications may occur sequentially on a single nucleotide. Secondary methylations of other modified residues in RNA, as well various derivatives of Y‐base (yW) formed by S‐adenosyl‐methonine (SAM)‐dependent methyltransferases (MTases) are also included in Panels (a) and (b). (b) Phylogenetic distribution of methylated nucleotides (all RNA species). (Reprinted with permission from Ref 5. Copyright 2005 Macmillan Reference Limited Stockton Press)

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Chemical structure of the most basic cap 0 structure m7G(5′)ppp(5′)N (left). Hypermethylated trimethylguanosine (right) is found, e.g., in the cap structures of snRNAs.

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Conventional view of guide RNA mediated methylation machinery in archaea (left) and Eukarya (right). sno(s)RNA guide is shown in black, the substrate RNA in red. Conserved sequences of boxes C, C′, D, D′ are indicated in black, the red asterisk indicates the position of 2′‐O‐methylation in the target RNA (red strand).

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Methylation sites in ribosomal RNA. (a) Modified nucleotides in 16S rRNA from Escherichia coli. Different modifications identified in E. coli 16S rRNA are shown as color‐filled circles. Pseudouridine residues are indicated in gray. Additional base and ribose methylations conferring antibiotic resistance are indicated in shaded boxes. (b) Modified nucleotides in 23S rRNA from E. coli. Different modifications identified in E. coli 23S rRNA are shown as color‐filled circles. Pseudouridine residues are indicated in gray. Additional base and ribose methylations conferring antibiotic resistance are indicated in shaded boxes.(c) Modified nucleotides in human 18S rRNA. Different modifications identified in human 18S rRNA are shown as color‐filled circles. Pseudouridine residues are indicated in gray. Locations of residues in gray rectangles were predicted based on the specificity of the respective snoRNA guides. (d) Modified nucleotides in human 28S rRNA. Different modifications identified in human 28S rRNA are shown as color‐filled circles. Pseudouridine residues are indicated in gray. Locations of residues in gray rectangles were predicted based on the specificity of the respective snoRNA guides.

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Methylated nucleotides in tRNA. Sites of nucleotide methylation indicated on the secondary cloverleaf structure of tRNA. The presence and identity of methylated residues are indicated for selected model organisms among bacteria (Escherichia coli), archaea (Halobacterium volcanii), and lower eukaryota (cytoplasmic tRNAs from Saccharomyces cerevisiae) for higher eukaryotic organisms, the cumulated picture from animal's cytoplasmic tRNAs is shown. Secondary methylations of other modified residues in RNA, as well as various derivatives of Y‐base (yW) formed by S‐adenosyl‐methonine (SAM)‐dependent MTases are also included. Universally conserved methylations are gray shaded, conserved in archaea and eukaryotes are in orange, and between bacteria and eukaryotes are in blue. m1Ψ in archaeal tRNAs is considered similar to m5U. (Reprinted with permission from Ref 5. Copyright 2005 Macmillan Reference Limited Stockton Press)

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Catalytic mechanisms of different MTases. (a) Trm5 enhances the nucleophilicity of N1 by deprotonation.18 (b) Michael addition of a catalytic cystein at C6 generates a C‐nucleophile enaminat/enolate in m5C MTases (reviewed in Ref 25). (c) Methylation of the 2 and 8 carbons in adenosine via radical S‐adenosyl‐methonine‐methyltransferases (SAM‐MTases).14

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