Optimization of a massively parallel genome editing approach to link regulatory elements to their target genes during mouse germ layer formation

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Cell fate diversification is part and parcel to mammalian development. With the completion of the Human Genome Project and subsequent large-scale efforts to functionally characterize the genome, we now know that coding and non-coding DNA interdependently affect cell fate decisions. High-throughout, largely descriptive assays carried out by the Encyclopedia of DNA Elements (ENCODE) Project and others like it, have contributed to an increasingly curated list of DNA and RNA regulatory elements associated with cell-type specific transcriptional and epigenetic programs. However, while it is estimated that 1 million cis-regulatory elements, presumably mostly enhancers, regulate the protein-coding genome, their identity and the genes they regulate remain largely unknown. Here, I propose to apply highly scalable functional approaches to candidate enhancer elements in a developmentally relevant and tractable system. Specifically, I am further developing a framework, known as 'massively parallel genome editing' or MPGE, that utilizes a CRISPR/Cas9 screening approach and single-cell RNA sequencing (scRNA-seq) to globally capture perturbations to gene expression. I will apply this method to mouse embryonic stem cell-derived germ layers, which are essential for body plan assembly in early development. Together, this study design will validate candidate enhancer elements in their native context while also identifying the target gene(s) that they regulate. This functional validation of germ layer-specific enhancer-gene pairs will yield insights into how cell fates emerge in early development.