ncRNAs: investigating functions and biogenesis

• Grant number: 24/09219-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: September 01, 2024
• End date: August 31, 2026
• Field of knowledge: Biological Sciences - Parasitology - Protozoology of Parasites
• Principal Investigator: Angela Kaysel Cruz
• Grantee: Flávio Henrique de Jesus Santos
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 23/03015-0 - Of epigenetics, genomic variability and gene expression regulation in Leishmania, AP.TEM

Abstract

In addition to their medical relevance, Leishmania parasites as early-branched organisms are excellent models for studying genetic and biochemical processes. The peculiarities of its genetic organization are remarkable; their genes are organized into long sets of directional clusters, and structural and functional polycistrons. There are no canonical promoters to control RNA polymerase II transcription of protein-coding genes devoid of introns. Therefore, a diversity of post-transcriptional regulatory factors and processes are central to regulating gene expression in this organism. In other organisms, non-coding RNAs (ncRNAs) have been assigned diverse and essential functions at different levels of the regulation of gene expression; from transcription to processing and controls of stability and translation rate of mRNAs. In the last decades, the so-called regulatory RNAs, still of imprecise classification, have been attributed functions as diverse as the sequestration of proteins to form specific lncRNA-protein complexes, the performance as signalers, enhancers, and guides, among others (Statello et al., 2021, Gil & Ulitsky, 2020, Mercer et al., 2009, Quinn & Chang, 2016). Different regulatory ncRNA classes have already been described in trypanosomatids (Michaeli et al., 2012, Kolev et al, 2019, Rajan et al, 2020).Regarding ncRNA functions and features in Leishmania, we are just touching the surface; their biological roles and their involvement in the parasite fitness allowing survival in both hostile environments must be investigated. Among the eleven thousand putative ncRNAs that we have identified in L. braziliensis, about three thousand are differentially expressed (Ruy et al, 2019). We pursued functional analysis and collected preliminary results for a small group of them. The selection included manual inspection of the locus to confirm the differential expression, preferentially presenting higher levels in infective stages, neighbor annotated features and profile of expression, and strength of prediction of the transcript as a ncRNA. We will aim to functionally investigate differentially expressed long ncRNAs (DE lncRNAs) and in parallel investigate their biogenesis. This Postdoctoral fellow's project aims to contribute to the functional studies on ncRNAs including (i) investigating the function of different categories of long ncRNAs (from intergenic regions and 3'UTR of mRNAs) and (ii) investigating the biogenesis of studied ncRNAs.