How cell fate becomes restricted during somatic cell differentiation is a 
long-lasting question in biology. Epigenetic mechanisms not present in 
pluripotent cells and acquired during embryonic development are expected to 
stabilize the differentiated state of somatic cells and thereby restrict their 
ability to convert to another fate. The histone variant macroH2A acts as a 
component of an epigenetic multilayer that heritably maintains the silent X 
chromosome and has been shown to restrict tumor development. Here we show that 
macroH2A marks the differentiated cell state during mouse embryogenesis. 
MacroH2A.1 was found to be present at low levels upon the establishment of 
pluripotency in the inner cell mass and epiblast, but it was highly enriched in 
the trophectoderm and differentiated somatic cells later in mouse development. 
Chromatin immunoprecipitation revealed that macroH2A.1 is incorporated in the 
chromatin of regulatory regions of pluripotency genes in somatic cells such as 
mouse embryonic fibroblasts and adult neural stem cells, but not in embryonic 
stem cells. Removal of macroH2A.1, macroH2A.2 or both increased the efficiency 
of induced pluripotency up to 25-fold. The obtained induced pluripotent stem 
cells reactivated pluripotency genes, silenced retroviral transgenes and 
contributed to chimeras. In addition, overexpression of macroH2A isoforms 
prevented efficient reprogramming of epiblast stem cells to naïve pluripotency. 
In summary, our study identifies for the first time a link between an epigenetic 
mark and cell fate restriction during somatic cell differentiation, which helps 
to maintain cell identity and antagonizes induction of a pluripotent stem cell 
state.