Yap1 safeguards mouse embryonic stem cells from excessive apoptosis during differentiation

While Yap1, a Hippo pathway transcriptional effector, plays numerous roles in development and cancer, its functions in embryonic stem (ES) cell differentiation remain poorly characterized. It is known that approximately 30% of ES cells die after exiting self-renewal to differentiate, but upstream regulators of this process are not well known. We first observe that ES cells lacking Yap1 experience massive cell death upon the exit from self-renewal. We subsequently reveal that Yap1 contextually protects differentiating, but not self-renewing, mouse ES cells from hyperactivation of the apoptotic cascade. Mechanistically, Yap1 strongly activates anti-apoptotic genes via directly occupying their regulatory elements while mildly suppressing pro-apoptotic genes. Our demonstration of the pro-survival functions of Yap1 during ES cell differentiation expands our understanding of upstream regulators of the balance between survival and death during cell fate changes. ChIP sequencing was performed for Yap1 in male mouse ES cells (strain J1). To perform ChIP-seq for Yap1, we generated Yap1-overexpressing FLAG/biotin-tagged clones, differentiated them for 3 days in ES- medium, and proceeded to formaldehyde-assisted crosslinking. Yap1 was pulled down along with associated DNA fragments using magnetic streptavidin-conjugated beads. ChIP-seq was also performed on BirA cells as a control, which express the BirA enzyme responsible for biotinylation, but do not overexpress any gene of interest.