In Silico Genetic Robustness Analysis of Secondary Structural Elements in the miRNA Gene

Heterogeneous ensemble approach with discriminative features and modified-SMOTEbagging for pre-miRNA classification

An ensemble classifier approach for microRNA precursor (pre-miRNA) classification was proposed based upon combining a set of heterogeneous algorithms including support vector machine (SVM), k-nearest neighbors (kNN) and random forest (RF), then aggregating their prediction through a voting system. Additionally, the proposed algorithm, the classification performance was also improved using discriminative features, self-containment and its derivatives, which have shown unique structural robustness characteristics of pre-miRNAs. These are applicable across different species. By applying preprocessing methods--both a correlation-based feature selection (CFS) with genetic algorithm (GA) search method and a modified-Synthetic Minority Oversampling Technique (SMOTE) bagging rebalancing method--improvement in the performance of this ensemble was observed. The overall prediction accuracies obtained via 10 runs of 5-fold cross validation (CV) was 96.54%, with sensitivity of 94.8% and specificity of 98.3%-this is better in trade-off sensitivity and specificity values than those of other state-of-the-art methods. The ensemble model was applied to animal, plant and virus pre-miRNA and achieved high accuracy, >93%. Exploiting the discriminative set of selected features also suggests that pre-miRNAs possess high intrinsic structural robustness as compared with other stem loops. Our heterogeneous ensemble method gave a relatively more reliable prediction than those using single classifiers. Our program is available at http://ncrna-pred.com/premiRNA.html.

Bioinformatic analysis of the neutrality of RNA secondary structure elements across genotypes reveals evidence for direct evolution of genetic robustness in HCV

The properties and origin of genetic robustness have recently been investigated in several works that examined microRNA stem-loop structures, and a variety of conclusions have been reached without agreement. Considering that this is a universal phenomenon that is not restricted to miRNAs, we recall the original work on this topic that began from looking at viral RNAs of several types. We provide a link to this work by examining the neutrality of HCV structural elements, performing a detailed bioinformatic analysis using RNA secondary structure predictions across genotypes. This study provides supporting evidence for direct evolution of genetic robustness that is not limited to noncoding RNAs participating in gene regulation, but includes functionally important structural elements of the hepatitis C virus (HCV) that show excess of robustness beyond the intrinsic robustness of their stem-loop structure. These findings further support the adaptive behavior of genetic robustness in functional RNAs of various types that seem to have evolved with selection pressure towards increased robustness.

Neutral evolution of robustness in Drosophila microRNA precursors

Mutational robustness describes the extent to which a phenotype remains unchanged in the face of mutations. Theory predicts that the strength of direct selection for mutational robustness is at most the magnitude of the rate of deleterious mutation. As far as nucleic acid sequences are concerned, only long sequences in organisms with high deleterious mutation rates and large population sizes are expected to evolve mutational robustness. Surprisingly, recent studies have concluded that molecules that meet none of these conditions--the microRNA precursors (pre-miRNAs) of multicellular eukaryotes--show signs of selection for mutational and/or environmental robustness. To resolve the apparent disagreement between theory and these studies, we have reconstructed the evolutionary history of Drosophila pre-miRNAs and compared the robustness of each sequence to that of its reconstructed ancestor. In addition, we "replayed the tape" of pre-miRNA evolution via simulation under different evolutionary assumptions and compared these alternative histories with the actual one. We found that Drosophila pre-miRNAs have evolved under strong purifying selection against changes in secondary structure. Contrary to earlier claims, there is no evidence that these RNAs have been shaped by either direct or congruent selection for any kind of robustness. Instead, the high robustness of Drosophila pre-miRNAs appears to be mostly intrinsic and likely a consequence of selection for functional structures.

Correlation between sequence conservation and structural thermodynamics of microRNA precursors from human, mouse, and chicken genomes

Background

Previous studies have shown that microRNA precursors (pre-miRNAs) have considerably more stable secondary structures than other native RNAs (tRNA, rRNA, and mRNA) and artificial RNA sequences. However, pre-miRNAs with ultra stable secondary structures have not been investigated. It is not known if there is a tendency in pre-miRNA sequences towards or against ultra stable structures? Furthermore, the relationship between the structural thermodynamic stability of pre-miRNA and their evolution remains unclear.

Results

We investigated the correlation between pre-miRNA sequence conservation and structural stability as measured by adjusted minimum folding free energies in pre-miRNAs isolated from human, mouse, and chicken. The analysis revealed that conserved and non-conserved pre-miRNA sequences had structures with similar average stabilities. However, the relatively ultra stable and unstable pre-miRNAs were more likely to be non-conserved than pre-miRNAs with moderate stability. Non-conserved pre-miRNAs had more G+C than A+U nucleotides, while conserved pre-miRNAs contained more A+U nucleotides. Notably, the U content of conserved pre-miRNAs was especially higher than that of non-conserved pre-miRNAs. Further investigations showed that conserved and non-conserved pre-miRNAs exhibited different structural element features, even though they had comparable levels of stability.

Conclusions

We proposed that there is a correlation between structural thermodynamic stability and sequence conservation for pre-miRNAs from human, mouse, and chicken genomes. Our analyses suggested that pre-miRNAs with relatively ultra stable or unstable structures were less favoured by natural selection than those with moderately stable structures. Comparison of nucleotide compositions between non-conserved and conserved pre-miRNAs indicated the importance of U nucleotides in the pre-miRNA evolutionary process. Several characteristic structural elements were also detected in conserved pre-miRNAs.

EvoRSR: an integrated system for exploring evolution of RNA structural robustness

Background

Robustness, maintaining a constant phenotype despite perturbations, is a fundamental property of biological systems that is incorporated at various levels of biological complexity. Although robustness has been frequently observed in nature, its evolutionary origin remains unknown. Current hypotheses suggest that robustness originated as a direct consequence of natural selection, as an intrinsic property of adaptations, or as a congruent correlate of environment robustness. To elucidate the evolutionary origins of robustness, a convenient computational package is strongly needed.

Results

In this study, we developed the open-source integrated system EvoRSR (Evolution of RNA Structural Robustness) to explore the evolution of robustness based on biologically important landscapes induced by RNA folding. EvoRSR is object-oriented, modular, and freely available at under the GNU/GPL license. We present an overview of EvoRSR package and illustrate its features with the miRNA gene cel-mir-357.

Conclusion

EvoRSR is a novel and flexible package for exploring the evolution of robustness. Accordingly, EvoRSR can be used for future studies to investigate the evolution and origin of robustness and to address other common questions about robustness. While the current EvoRSR environment is a versatile analysis framework, future versions can include features to enhance evolutionary studies of robustness.