Studying the exit from pluripotency and identifying key factors that regulate differentiation outcomes

Gene expression heterogeneity of mouse embryonic stem cells (mESCs) naïve and primed states has been characterized. However, exit from pluripotency and lineage commitment have not been directly linked with mESCs states. The most prominent variation between mESCs single cell RNAseq data reflected by cell cycle states. My previous work linked cell cycle states with average tendencies towards cell-fate decisions. However, as bulk RNA experiments is blind to cell-to-cell variation, we combined cell cycle and single cell RNAseq measurements to improve our capacity to link between mESCs cell cycle states and differentiation outcomes. I showed that ESRRB is a key factor over expressed during G2/M state and associates with extra embryonic endoderm (XEN) differentiation. Now I expand the search for other cell cycle sensitive regulators using a systematic CRISPR screen and identified Jarid2 as a prominent candidate using functional studies.

Finally, to overcome batch effect that might inhibit our ability to systematically compare between single cell assays, I will attempt to develop a CRISPR based `scaring` method that will allow us to mix cells from different genetic background in one single cell RNAseq experiment and de-convolute cells back to their original experiment after sequencing. This will allow us to overcome batch-based variation which is a major confounder across single cell experiments.