title: Deciphering RNA Regulatory Elements Involved in the Developmental and Environmental Gene Regulation of Trypanosoma brucei.
abstract: Trypanosoma brucei is a vector-borne parasite with intricate life cycle that can cause serious diseases in humans and animals. This pathogen relies on fine regulation of gene expression to respond and adapt to variable environments, with implications in transmission and infectivity. However, the involved regulatory elements and their mechanisms of actions are largely unknown. Here, benefiting from a new graph-based approach for finding functional regulatory elements in RNA (GRAFFER), we have predicted 88 new RNA regulatory elements that are potentially involved in the gene regulatory network of T. brucei. We show that many of these newly predicted elements are responsive to both transcriptomic and proteomic changes during the life cycle of the parasite. Moreover, we found that 11 of predicted elements strikingly resemble previously identified regulatory elements for the parasite. Additionally, comparison with previously predicted motifs on T. brucei suggested the superior performance of our approach based on the current limited knowledge of regulatory elements in T. brucei.
authors.affiliation: Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Montreal, Quebec, Canada.
authors.forename: Vahid H
authors.initials: VH
authors.lastname: Gazestani
authors.affiliation: Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Montreal, Quebec, Canada; McGill Centre for Bioinformatics, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada; Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada.
authors.forename: Reza
authors.initials: R
authors.lastname: Salavati
mesh_terms: D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D016053:RNA, Protozoan / Q000096:biosynthesis / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid; D014346:Trypanosoma brucei brucei / Q000235:genetics* / Q000378:metabolism
chemical_list: D016053:RNA, Protozoan; D038621:Regulatory Sequences, Ribonucleic Acid