H2A.X native ChIP-Seq in TSC; Histone Variant H2A.X Mediated Epigenetic Mechanisms are Critical for Pluripotency in ES and iPS Cells

With the advent of the induced pluripotent stem cell (iPSC) technology, how to distinguish the developmental potentials of the iPSC clones with molecular approaches becomes an imperative issue. Herein, we demonstrated that histone variant H2A.X plays an unexpected role in distinguishing the developmental potentials of iPSC. We showed that H2A.X is specifically targeted to and negatively regulates extra-embryonic lineage gene expression in embryonic stem cell (ESCs) and therefore, it prevents trophectoderm (TE) lineage differentiation under inductive conditions. ESC-specific H2A.X deposition and functions are faithfully recapitulated in the iPSC lines that support the development of “all-iPS” animals. In iPSC lines that fail to support embryonic development, aberrant H2A.X depositions result in upregulation of extra-embryonic lineage genes and predisposition to extra-embryonic tissue differentiation. In summary, our work has revealed novel epigenetic mechanisms for maintaining cell lineage commitment, which can be used to distinguish the quality of the iPSC lines.