Inferring new gene regulatory networks in Trypanosoma cruzi based on multiple integrated data sources using bioinformatic analysis

SABALETTE, KB; DE GAUDENZI, JG

Mendoza

Congreso; XI Congreso SAP 2022; 2022

Sociedad Argentina de Protozoología

Trypanosoma cruzi, the agent of Chagas disease, mostly regulates protein synthesis by post-transcriptional events. These mechanisms involve RNA-binding proteins (RBPs) that bind to RNA sequences. Here we developed a computational pipeline to reliably predict RBP-RNA interactions in trypanosomes. For this purpose, we integrated five published datasets containing more than 150 RNA motifs of T. cruzi. These motifs are: elements experimentally obtained by our lab (set 1); predicted from metabolic pathways (set 2); derived from groups of RNAs co-expressed during parasite development (set 3) or upon hyperosmotic stress (set 4), and identified during the cell cycle progression (set 5). Firstly, these RNA elements were used as a query to search for eukaryotic proteins with the ability to bind them according to TOMTOM motif analysis (https://meme-suite.org/meme/tools/tomtom, MEME suite). Using an FDR of 5%, heterologous interacting proteins were predicted by searching against the RNA compete database composed of 244 eukaryotic RBPs. In the second step, hundreds of highly similar T. cruzi proteins were identified as binders of the mentioned RNA motifs (groups 1 to 5) by using the BLASTp program against trypanosome RBP databases. Next, the RPIseq prediction program (http://pridb.gdcb.iastate.edu/RPISeq/) was run to select those confident interactions that have binding probabilities >0.5 utilizing RF and SVM classifiers. After these simple steps, the results were displayed employing network graphs in R (https://igraph.org/r/), and examined using common network analysis parameters, to visualize connections among 72 RBPs that putatively interact with 60 RNA motifs, totaling 1053 different interactions. We consider that this novel trypanosome RBP-RNA catalog lays out the foundation required for further functional characterization of gene regulatory networks in the T. cruzi pathogen.