Locations of several novel 2'-O-methylated nucleotides in human 28S rRNA - PubMed (original) (raw)

Locations of several novel 2'-O-methylated nucleotides in human 28S rRNA

Ana Rebane et al. BMC Mol Biol. 2002.

Abstract

Background: Ribose 2'-O-methylation, the most common nucleotide modification in mammalian rRNA, is directed by the C/D box small nucleolar RNAs (snoRNAs). Thus far, more than fifty putative human rRNA methylation guide snoRNAs have been identified. For nine of these snoRNAs, the respective ribose methylations in human 28S rRNA have been only presumptive.

Results: In this study, the methylation state of human 28S rRNA in the positions predicted by the snoRNAs U21, U26, U31, U48, U50, U73, U74, U80 and U81 was assessed using reverse transcription-based methods and several novel 2'-O-methylations were localized.

Conclusions: Seven novel ribose 2'-O-methylated residues (Am389, Am391, Gm1604, Gm1739, Gm2853, Cm3810, Gm4156, predicted by snoRNAs U26, U81, U80, U73, U50, U74 and U31, respectively) have been localized in human 28S rRNA. The total number of 2'-O-methylations in human rRNA is not yet known.

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Figures

Figure 1

Figure 1

Location of novel 2'-_O_-methylated nucleotides in human 28S rRNA using reverse transcription of partially hydrolyzed rRNA and reverse transcription of rRNA at low dNTP concentrations. The positions of novel 2'-O-methylated nucleotides are shown in bold together with the putative snoRNA guide in parenthesis. Three previously detected methylations Cm2838, Am3794 and Am3799 are also indicated. Lanes 0', 30', 45' and 60' show primer extension products of partially hydrolyzed 28S rRNA, where the hydrolysis time is 0, 30, 45 and 60 min, respectively. Lanes, labeled 1 mM, 0.02 mM and 0.002 mM represent reverse transcription products of 28S rRNA at the indicated dNTP concentrations. Lanes A, C, G and T contain dideoxy sequencing ladders. Note that primer extension products generated with 5'-end-phosphorylated oligodeoxynucleotide primers migrate about 1 nucleotide farther than the respective sequencing reaction products produced with oligodeoxynucleotide primers bearing a hydroxyl group at the 5' end and terminating with dideoxynucleotides.

References

    1. Maden BE. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1990;39:241–303. - PubMed
    1. Nicoloso LH, Qu B, Michot B, Bachellerie JP. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs. J Mol Biol. 1996;260:178–195. doi: 10.1006/jmbi.1996.0391. - DOI - PubMed
    1. Kiss-László Z, Yves H, Bachellerie J-P, Caizergues-Ferrer M, Kiss T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell. 1996;85:1077–1088. - PubMed
    1. Bachellerie JP, Cavaillé J. Small nucleolar RNAs guide the ribose methylations of eukaryotic rRNAs. In: Grosjean H, Benne R, editor. Modification and editing of RNA. Washington, ASM Press; 1998. pp. 255–272.
    1. Smith CM, Steitz JA. Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5'-terminal oligopyrimidine gene family reveals common features of snoRNA host genes. Mol Cell Biol. 1998;18:6897–6909. - PMC - PubMed

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