Functional Characterization of long noncoding RNAs in Innate Immunity 2204

Abstract Description There are ∼20,000 annotated long noncoding RNAs (lncRNAs) in the human genome with only a small percentage having ascribed functions. Here I present our approaches to functionally characterize conserved lncRNAs. We are focused specifically on the role that lncRNAs play in regulating macrophage biology. Macrophages are critical to a well-functioning immune response and first we have employed CRISPRi-based pooled screening to rapidly identify which lncRNAs function during macrophage differentiation and inflammatory responses. In total we have identified 73 regulators and performed in depth functional analysis of the top hit from both screens, LOUP [lncRNA originating from upstream regulatory element of SPI1 (also known as PU.1)]. We showed that LOUP regulates SPI1 in cis in a highly conserved manner. We have identified small open reading frames-encoded peptides that are produced from the LOUP locus that negatively regulate the TLR4-NFkB signaling cascade. By studying lncRNAs conserved between species it enables us to generate mouse models to further validate the roles that lncRNAs play in vivo. We have taken this approach specifically to study two lncRNAs, lincRNA-Cox2 and GAPLINC and using knockout and overexpression models we have gained insights into their specific functions in the regulation of macrophages. In conclusion by utilizing CRISPR screening and genetic mouse models we have gained new insights into the roles that lncRNAs play in regulating innate immunity. Funding Sources R35GM137801 from NIGMS R01 AI148413 from NIAID Topic Categories Innate Immune Responses and Host Defense: Molecular Mechanisms (INM)