Characterization of Plasmodium falciparum long non-coding RNAs and their roles in gene regulation

Abstract Malaria remains a major public health problem worldwide and, partially due to our incomplete understanding of the biology of Plasmodium falciparum, our progress towards eradicating the disease has stalled in recent years. Long non-coding RNAs (lncRNAs) have emerged as a key component of gene regulation in eukaryotes, influencing both the transcription of genes and the stability and translation of mRNAs. While specific lncRNAs have been shown to regulate pathogenesis and parasite development, we still lack a comprehensive perspective on the importance of lncRNAs in P. falciparum. Here, we propose to use a combination of state-of-the-art genomic and molecular approaches to examine the role of lncRNAs in gene regulation and their modes of action. First, we propose to evaluate, at the genome scale, how lncRNAs influence the regulation of gene expression of neighboring and distant genes using a suite of computational approaches and novel genomic assays. Second, we will comprehensively examine the role of a new antisense lncRNA located downstream of ap2-g, the gene that encodes a transcription factor that acts as the master regulator of sexual commitment in malaria parasites. To do this, we will generate genetically modified parasite lines which modulate the levels of the ap2-g lncRNA using a variety of molecular approaches and we will phenotypically characterize the resulting effects on both asexual and sexual blood stage malaria parasite development. Overall, the proposed analyses will provide novel insights into the roles of lncRNAs in gene regulation in Plasmodium parasites. The results of this proposal will lay the foundation for future studies aimed at characterizing additional well-curated, and developmentally regulated P. falciparum lncRNAs.