Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
Open Access
- 2 March 2009
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 37 (8), 2461-2470
- https://doi.org/10.1093/nar/gkp093
Abstract
Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post-transcriptional modifications or RNA editing. Modifications include N 1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3′ micro RNA uridine extensions and 5′ micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5′ deletions and 3′ uridine extensions can alter the specificity by which micro RNAs associate with different Argonaute proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post-transcriptional RNA modifications.Keywords
This publication has 54 references indexed in Scilit:
- Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal NucleotideCell, 2008
- SOAP: short oligonucleotide alignment programBioinformatics, 2008
- Conserved amino acids in each subunit of the heteroligomeric tRNA m 1 A58 Mtase from Saccharomyces cerevisiae contribute to tRNA bindingNucleic Acids Research, 2007
- miRNA Editing—We Should Have Inosine This ComingMolecular Cell, 2007
- Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylationNature, 2006
- RNA editing in plant organelles: machinery, physiological function and evolutionCellular and Molecular Life Sciences, 2006
- Modulation of microRNA processing and expression through RNA editing by ADAR deaminasesNature Structural & Molecular Biology, 2005
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic SequenceNucleic Acids Research, 1997
- Sequence logos: a new way to display consensus sequencesNucleic Acids Research, 1990