Non-coding small RNA discovery from -omics data

KAMENETZKY, L.

Workshop; II Reunión Argentina de Biología de ARNs no codificantes; 2018

Several complete genome sequences have been recently obtained. Annotation efforts are usually focused in analyzing protein-coding genes, but there is still a vast proportion of the genome that needs to be explored, including non-coding RNAs such as small RNAs. microRNAs (miRNAs) are a class of small regulatory RNAs identified in many different organisms ranging from viruses to higher eukaryotes. MiRNAs are key regulators of gene expression at post-transcriptional level and play important roles in biological processes such as development, proliferation, cell differentiation and metabolism in animals and plants. In spite of this, identification of miRNAs directly from genome-wide data is still a very challenging task. There are several miRNAs that remain unidentified due to the lack of either sequence information of particular phyla or appropriate algorithms to identify novel miRNAs. The motivation of our work is the discovery of new miRNAs in non-model species, based on non-target genomic data only, in order to obtain useful information from the currently available unexplored data. We present a new algorithm (miRNA-SOM) for the discovery of pre-miRNAs which was implemented over whole genome data allowing to describe ~ 30 conserved miRNA families within platyhelminth parasites and the remarkable loss of some miRNAs from mammals, reflecting their adaptation to parasitism. Predictions were meaningful using only sequence data, with no need of RNA-seq data or target analysis for prediction. We compared our new approach with the small non-coding RNAs searching strategies that have been mostly used in literature in recent years