Genome-scale discovery of protein-coding and lncRNA gene function with CRISPRi and CRISPRa

The genome sequencing efforts of the past decade have cataloged the universe of protein-coding and non-coding transcripts produced by the human genome. A central challenge now is to understand how these many thousands of genes act to mediate the vast array of cellular processes involved in either normal or disease states. To accomplish this, we require specific and scaleable tools to manipulate the expression of individual genes and measure their functional contribution in a given cellular context. In this thesis, I describe the initial development and subsequent refinement of genome-scale genetic screening technologies based on CRISPR-mediated interference and activation. I present the results of several screens for protein-coding genes that modulate cell proliferation and toxin susceptibility. Finally, I describe the application of CRISPR interference in the systematic repression of long non-coding RNA genes, a large class of genes of which very few genes have any known function. The screens described here identify nearly 500 lncRNA genes that modify cell growth in at least one of seven diverse cell lines, and furthermore highlight the exquisite cell type-specificity of lncRNA function