In recent years, the discovery of numerous non-coding (nc)RNAs has dramatically changed the view of how organisms control their biological processes. Small ncRNAs such as micro(mi)RNAs and small interfering (si)RNAs have been explored mainly in multicellular organisms, i.e. plants and animals, where they are crucial to ensure proper gene expression. Other classes of ncRNAs have also been demonstrated to play important roles in different biological processes.
The focus of my research is to understand the role of ncRNAs, using bioinformatics and experimental methodology. We previously identified an abundant and highly expressed class of ncRNA (Class I RNAs), 42 – 65 nt long, involved in multicellular development in the social amoeba Dictyostelium discoideum. In order to understand if Class I RNAs are unique to D. discoideum or also present in other organisms, we searched for Class I RNA genes in genomes from species representing each major group of dictyostelid social amoeba. Numerous Class I RNA genes were identified in all of these species, which separated from their last common ancestor some 600 million years ago. In contrast, genomes from strictly unicellular Amoebozoa showed no evidence of this class of RNA. Analysis of Class I RNAs from the different social amoeba species revealed several conserved features. They harbor a short stem-structure, connecting the 5´ and 3´ ends, and a conserved sequence element. In addition, the genes are preceded by a putative promoter sequence. Based on apparent lack of synteny and analysis of primary sequence, it appears as if the expansion of Class I RNA genes took place largely after the divergence of Dictyostelia. Hence, our results show that Class I RNA is an ancient abundant class of ncRNA, likely specific to dictyostelid social amoeba, and could play a role in their evolution and unique multicellular life style.
We are also interested in the function of mi- and siRNAs using D. discoideum as a model. Utilizing different high throughput sequencing methods, we have identified numerous mi- and siRNAs in D. discoideum. We are presently investigating their targets, evolution, role in gene regulation, and their associated protein factors.