Chemical secondary structure probing of two highly methylated regions in Xenopus laevis 28S ribosomal RNA

NmRF: identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences

2'-O-methylation (Nm) is a post-transcriptional modification of RNA that is catalyzed by 2'-O-methyltransferase and involves replacing the H on the 2'-hydroxyl group with a methyl group. The 2'-O-methylation modification site is detected in a variety of RNA types (miRNA, tRNA, mRNA, etc.), plays an important role in biological processes and is associated with different diseases. There are few functional mechanisms developed at present, and traditional high-throughput experiments are time-consuming and expensive to explore functional mechanisms. For a deeper understanding of relevant biological mechanisms, it is necessary to develop efficient and accurate recognition tools based on machine learning. Based on this, we constructed a predictor called NmRF based on optimal mixed features and random forest classifier to identify 2'-O-methylation modification sites. The predictor can identify modification sites of multiple species at the same time. To obtain a better prediction model, a two-step strategy is adopted; that is, the optimal hybrid feature set is obtained by combining the light gradient boosting algorithm and incremental feature selection strategy. In 10-fold cross-validation, the accuracies of Homo sapiens and Saccharomyces cerevisiae were 89.069 and 93.885%, and the AUC were 0.9498 and 0.9832, respectively. The rigorous 10-fold cross-validation and independent tests confirm that the proposed method is significantly better than existing tools. A user-friendly web server is accessible at http://lab.malab.cn/∼acy/NmRF.

Identifying 2'-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions

2'-O-methylationation is an important post-transcriptional modification and plays important roles in many biological processes. Although experimental technologies have been proposed to detect 2'-O-methylationation sites, they are cost-ineffective. As complements to experimental techniques, computational methods will facilitate the identification of 2'-O-methylationation sites. In the present study, we proposed a support vector machine-based method to identify 2'-O-methylationation sites. In this method, RNA sequences were formulated by nucleotide chemical properties and nucleotide compositions. In the jackknife cross-validation test, the proposed method obtained an accuracy of 95.58% for identifying 2'-O-methylationation sites in the human genome. Moreover, the model was also validated by identifying 2'-O-methylation sites in the Mus musculus and Saccharomyces cerevisiae genomes, and the obtained accuracies are also satisfactory. These results indicate that the proposed method will become a useful tool for the research on 2'-O-methylation.

Mapping 2'-O-methyl groups in ribosomal RNA

Ribosomal RNAs (rRNAs) from all sources contain modified nucleosides, whose numbers range from a few in mitochondrial rRNA to more than 200 in the complete rRNAs of some higher eukaryotes. In eukaryotic rRNA the great majority of modified nucleosides are 2'-O-methylated nucleosides or pseudouridines. The locations of most of the 2'-O-methylated nucleosides in rRNA from some representative eukaryotes are known from studies whose aim was full characterization of rRNA methylation. More recently, and particularly in connection with the discovery of methylation guide RNAs, it is often required to check for the presence or absence of 2'-O-methyl nucleosides at specified locations within rRNA. Three methods that can be applied for such "local" objectives are reviewed. Two of the methods are based on primer extension by reverse transcriptase. They exploit, respectively, a tendency of 2'-O-methyl groups to impede reverse transcriptase at low dNTP concentrations, or the resistance of phosphodiester bonds adjacent to 2'-O-methyl groups to alkaline hydrolysis. Examples of these methods are summarized. Although the two methods are relatively straightforward, they suffer from various experimental limitations, as discussed. The third method is technically more sophisticated but is capable of overcoming the limitations of the first two methods. It is based on the resistance of a target 2'-O-methylated site to cleavage by RNase H when the site is hybridized to an appropriate chimeric oligonucleotide. An overview of the approaches and methods now available for the complete mapping of 2'-O-methyl groups in rRNA is presented.