title: Deciphering RNA regulatory elements in trypanosomatids: one piece at a time or genome-wide?
abstract: Morphological and metabolic changes in the life cycle of Trypanosoma brucei are accomplished by precise regulation of hundreds of genes. In the absence of transcriptional control, RNA-binding proteins (RBPs) shape the structure of gene regulatory maps in this organism, but our knowledge about their target RNAs, binding sites, and mechanisms of action is far from complete. Although recent technological advances have revolutionized the RBP-based approaches, the main framework for the RNA regulatory element (RRE)-based approaches has not changed over the last two decades in T. brucei. In this Opinion, after highlighting the current challenges in RRE inference, we explain some genome-wide solutions that can significantly boost our current understanding about gene regulatory networks in T. brucei.
authors.affiliation: Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Sainte Anne de Bellevue, Montreal, Quebec H9X3V9, Canada.
authors.forename: Vahid H
authors.initials: VH
authors.lastname: Gazestani
authors.affiliation: Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Sainte Anne de Bellevue, Montreal, Quebec H9X3V9, Canada.
authors.forename: Zhiquan
authors.initials: Z
authors.lastname: Lu
authors.affiliation: Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Sainte Anne de Bellevue, Montreal, Quebec H9X3V9, Canada; McGill Centre for Bioinformatics, McGill University, Duff Medical Building, 3775 University Street, Montreal, Quebec H3A2B4, Canada; Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec H3G1Y6, Canada. Electronic address: reza.salavati@mcgill.ca.
authors.forename: Reza
authors.initials: R
authors.lastname: Salavati
mesh_terms: D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics*; D055106:Genome-Wide Association Study; D012313:RNA / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D014351:Trypanosomatina / Q000235:genetics*
chemical_list: D012313:RNA
keywords: RNA binding proteins; RNA regulatory elements; regulatory networks; trypanosomes