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Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs.
- Source :
-
PLoS genetics [PLoS Genet] 2013 Jun; Vol. 9 (6), pp. e1003602. Date of Electronic Publication: 2013 Jun 27. - Publication Year :
- 2013
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Abstract
- The presence of 5-methylcytidine (m(5)C) in tRNA and rRNA molecules of a wide variety of organisms was first observed more than 40 years ago. However, detection of this modification was limited to specific, abundant, RNA species, due to the usage of low-throughput methods. To obtain a high resolution, systematic, and comprehensive transcriptome-wide overview of m(5)C across the three domains of life, we used bisulfite treatment on total RNA from both gram positive (B. subtilis) and gram negative (E. coli) bacteria, an archaeon (S. solfataricus) and a eukaryote (S. cerevisiae), followed by massively parallel sequencing. We were able to recover most previously documented m(5)C sites on rRNA in the four organisms, and identified several novel sites in yeast and archaeal rRNAs. Our analyses also allowed quantification of methylated m(5)C positions in 64 tRNAs in yeast and archaea, revealing stoichiometric differences between the methylation patterns of these organisms. Molecules of tRNAs in which m(5)C was absent were also discovered. Intriguingly, we detected m(5)C sites within archaeal mRNAs, and identified a consensus motif of AUCGANGU that directs methylation in S. solfataricus. Our results, which were validated using m(5)C-specific RNA immunoprecipitation, provide the first evidence for mRNA modifications in archaea, suggesting that this mode of post-transcriptional regulation extends beyond the eukaryotic domain.<br />Competing Interests: The authors have declared that no competing interests exist.
- Subjects :
- Archaea genetics
Bacillus subtilis genetics
Cytidine genetics
Escherichia coli genetics
Gene Expression Profiling
Genome
High-Throughput Nucleotide Sequencing
Saccharomyces cerevisiae genetics
Cytidine analogs & derivatives
Methylation
RNA, Messenger genetics
RNA, Ribosomal genetics
RNA, Transfer genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1553-7404
- Volume :
- 9
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- PLoS genetics
- Publication Type :
- Academic Journal
- Accession number :
- 23825970
- Full Text :
- https://doi.org/10.1371/journal.pgen.1003602