Genome-wide search for regulatory RNA elements in clusters of metabolically related transcripts in trypanosomes

DE GAUDENZI, JG; CARMONA, S; AGÜERO, F; FRASCH, AC

Córdoba

Congreso; 2do Congreso Argentino de Bioinformática y Biología Computacional 2011; 2011

A2B2C

BackgroundIn eukaryotic cells, a group of functionally related mRNAs together with the trans-acting factors that coordinately modulate their expression is termed a post-transcriptional regulon, due to their partial analogy to the polycistronic mRNAs of bacteria. Current evidence indicates that these post-transcriptional networks or RNA regulons govern gene expression in trypanosomes, and individual reports have revealed the existence of post-transcriptional regulons in these microorganisms.ResultsTo assess if  UTRs in a set of mRNAs contain common sequence elements, we grouped trypanosomatid genes from complete genomes into several metabolic categories according to the KEGG pathways database,and then searched for conserved RNA stem-loops in their 3´UTRs . Next, candidate motifs were used to build stochastic context-free grammar models that were used to search for matching sequences in all  KEGG groups. Interestingly, 26 of 53 KEGG categories showed significant enrichment of conserved structural RNA motifs in comparison with a control group composed by randomly selected 3´UTRs. An analysis of RNA motif coverage against 18 distinct datasets that did not share any transcripts (non-overlapped groups) showed that, in general, each cis-element was more abundant in the corresponding (self) dataset than in the remaining groups (see Figure 1). Additionally, two motifs displayed a widespread distribution, and were located in virtually all 3´UTR sequences.ConclusionIn this work we globally identified candidate individual components for the mRNP-driven organization of distinct coordinately regulated cohorts of transcripts in trypanosomes. Using a bioinformatics strategy we describe signature RNA stem-loop motifs in the 3´UTRs of functionally related transcripts, thus supporting the post-transcriptional regulon´s model. Although most 3´UTR signature elements were group-specific, two motifs have a broad distribution, suggesting a putative role in post-transcriptional mRNA processing.