High throughput CRISPR-mediated functional validation of regulatory elements

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Project Summary The overarching goal of the proposed study is to functionally characterize a large number of candidate functional elements in the mammalian genome. The ENCODE projects have revealed millions of putative regulatory elements across more than one hundred cell types and tissues. While these maps have significantly expanded our knowledge of non-coding sequences, there are still large gaps between having descriptive maps of functional elements and understanding the biology of these elements underlying gene regulation. These include: (a) few candidate functional elements predicted by the ENCODE experiments are functionally validated; (b) Epigenomic studies have not given/revealed information on the target genes of candidate functional elements. Therefore, it is still a challenge to interpret the biological functions of non-coding DNA sequences. To address these issues, the objective of this UM1 application is to perform large scale functional characterization of candidate functional elements in their native chromatin context. We will first identify candidate regulatory elements utilizing ENCODE data and generate reporter tagged genes of interest in cell lines utilizing a high throughput, automated platform. Second, we will interrogate candidate functional elements in their native chromatin contexts utilizing two complementary high throughput CRIPSR/Cas9 mediated genome editing approaches. We anticipate these analyses will significantly advance our knowledge of the biological functions of candidate regulatory regions and gene regulation in mammalian cells.