Systematic computational analysis of potential RNA interference regulation in Toxoplasma gondii

Abstract

RNA-mediated silencing was first described in plants and became famous by studies in Caenorhabditis elegans. RNA interference (RNAi) is the mechanism through which an RNA interferes with the production of other RNAs in a sequence specific manner. MiRNAs are a type of RNA which originate from the genome with their active form being ss-RNAs of 21-23 nucleotides in length. They are being transcribed as primiRNAs then processed in the nucleus by Drosha to pre-miRNAs with a stem-loop structure and 70 nucleotides in length. This stem-loop containing pre-miRNAs is then processed in the cytoplasm to ds-RNA one strand of which will serve as interfering RNA. Toxoplasma gondii is a species of parasitic protozoa which causes several diseases. T.gondii emerges as a good candidate for computational efforts with its small genome size, publicly available genome files and extensive information about its gene structure, either based on experimental data or the prediction with several gene finders in parallel. Therefore, it seems important to establish the regulatory network composed of RNAi which may be beneficial for the Toxoplasma community. Within this context the pool of possible stem-loop constitutive transcripts are produced, further analysis of this pool for desired 2D structure is integrated and mapping of possible RNAi regulation to T.gondii.s genome is established. In connection with computational assessment and mapping, the derived information is provided as a database for quick lookup using a convenient web interface for experimental studies of RNAi regulation in Toxoplasma, thus reduce time and money costs in such studies.