Computational identification and structural characterization of non-coding RNA in Leishmania braziliensis

Abstract

The genetic organization of the protozoan parasite Leishmania braziliensis, similarly to other trypanosomatids, differs markedly from most eukaryotes. It has a compact genome, and its approximately 9,000 protein-coding genes are transcribed, without canonical promoters, as polycistronic units that rely on trans-splicing for the production of mature mRNAs. This genetic organization largely transfers control of gene expression to the post-transcriptional level. There is much to be investigated on the molecular mechanisms and factors involved in the post-transcriptional regulatory steps. Our laboratory has a central interest in studying some of these factors and mechanisms. Among them, we are investigating and already identified a large number of putative non-protein coding RNAs (ncRNA) as potential regulatory elements. In the present project, we intend to explore the content of putative ncRNAs in L. braziliensis employing computational approaches recently developed by the Danish group led by J. Gorodkin, a collaborator in this proposal. In this work, we will use their innovative in silico methodologies to classify putative ncRNAs of Leishmania based on the structure. The approach to be applied combines two strategies for genome-wide screens of structured RNAs. The strategies of simultaneously folding and aligning RNA (structural alignment) allow reaching more in-depth than the screens based on first constructing a sequence-based alignment and then structure search on top of this. This combined strategy is supported by the conservation of the ncRNA structures identified in evolutionarily related species. Besides, methods of clustering of conserved RNA structures will be used, opening the potential to discover RNA families sharing the same structure. The analysis of the structure-based RNA clusters confers a rational basis to select subpopulations of ncRNAs to be further investigated, by reverse genetics. (AU)