High throughput functional characterization of lncRNAs in macrophage biology

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Project Summary In this proposal we combine a number of technological approaches to provide a novel way to functionally characterize complex gene networks to identify those that function to regulate biological processes in macrophages. Advances in deep sequencing technologies have revealed that the majority of the human genome is actively transcribed into RNA. Our lab is focused on characterizing the largest group of RNA produced from the genome named long noncoding RNA (lncRNAs) and their associated protein binding partners. To date only 3% of lncRNAs have been functionally validated. This project is highly innovative as we will perform the first systematic unbiased screens and create the first genetic interaction maps to identify functionally relevant lncRNAs involved in viability and functions within macrophages. Using our newly developed reporter cell lines in both human and mouse we will be able to rapidly screen and map for lncRNAs and their protein binding partners that are critical for controlling viability and inflammatory signaling. We will also obtain crucial information on functional conservation of lncRNAs across species. We will then create genetic mouse models to prove the importance of these genes and their regulatory networks in controlling immune responses during sepsis in vivo. This approach will allow for rapid meaningful data to be obtained in a highly efficient manner. Accomplishing the ambitious goals of this proposal will provide us with a wealth of information on the complex pathways involving lncRNAs and gain insights into their roles in contributing to viability and functions of macrophages.