Technological advances in RNA sequencing have led to the view that the human genome is pervasively transcribed, resulting in the production of thousands of long non-coding RNAs (lncRNAs). A few lncRNAs are now recognized as key components of diverse physiological processes. However, molecular genetics lacks a more comprehensive view of lncRNome functionality and the mechanistic basis through which lncRNAs operate.
Therefore, I will establish a novel workflow and technologies to systematically characterize four cellular readouts and a molecular profile describing all possible functional associations of hundreds of lncRNAs in various cancer cell line models. CRISPR interference-based lncRNA loss-of-function screening will be conducted in high-throughput to assess cell proliferation, apoptosis, migration and differentiation in parallel. This strategy evaluates hundreds of lncRNA perturbations in a single effort. Cellular phenotypes will be complemented with molecular phenotypes through RNA sequencing of each lncRNA perturbation, providing the most systematic and comprehensive analysis of lncRNA function to date. Various lncRNA features including conservation across species, expression specificity to the model, splicing efficiency and super-enhancer association will be evaluated for their ability to predict lncRNA functionality.