Year 3

The application of human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) requires reliable cell sources that do not change over time and initiate proper transcriptional and chromatin changes upon induction of differentiation. However, female hESCs and hiPSCs exhibit an epigenetic instability of the X chromosome. Therefore, it is important to systematically define the epigenetic abnormalities that hESCs and hiPSCs carry, to understand how and when the epigenetic instability of the X chromosome arises during the derivation of these cells, to define the consequences if the different X chromosome states for differentiation, and to find ways to overcome the epigenetic instability. To this end, we have applied a large number of single cell, genome-wide, and population-wide approaches to understand this problem at a systematic and comprehensive level. Our findings define the relationship between different X-inactivation states in female hESCs and hiPSCs and demonstrate the consequences of different X-inactivation states for differentiation. Moreover, we have developed a strategy that erases the instability of the inactive X chromosome and enables faithful X chromosome dosage compensation in differentiating hESCs and hiPSCs, which is critical for the use of these cells in regenerative medicine, disease studies, and basic research.