Enhancer of Rudimentary Homolog (ERH) is an evolutionarily conserved
protein originally characterized as promoting fission yeast
heterochromatin and recently shown to maintain H3K9me3 heterochromatin
in human fibroblasts. Here, we find that ERH depletion in fibroblasts
reverts the somatic cell H3K9me3 landscape of broad megabase size
domains to an embryonic stem cell (ESC) state composed of mainly H3K9me3
peaks and enables activation of naïve and pluripotency genes and
transposable elements during induced pluripotent stem cell (iPSC)
reprogramming. Concordantly, we find that ERH represses totipotent and
alternative lineage programs during mouse preimplantation development
and is required for proper segregation of the inner cell mass and
trophectoderm cell lineages. During human ESC differentiation into germ
layer lineages, ERH silences naïve and pluripotency genes, transposable
elements, and alternative lineage somatic genes. As in fission yeast, we
find that mammalian ERH interacts with RNA-binding proteins to engage
and repress its chromatin targets. Our findings reveal a conserved,
fundamental role for ERH in mammalian cell fate specification via the
initiation and maintenance of early developmental gene repression.