Base editing-mediated R17H substitution in histone H3 reveals its methylation-dependent regulation of Yap signaling and early mouse embryo development

The coactivator-associated arginine methyltransferase CARM1 catalyzes the methylation of histone H3 arginine 17/26 and non-histone proteins at arginine residues. Through global mapping of H3 arginine methylation (H3Rme) enrichment or Carm1 overexpression assays, H3Rme has been revealed to be involved in gene transactivation in cultured human cells and pluripotency regulation in the mouse preimplantation embryo. However, the direct relationship between H3Rme and its causal role in early mouse embryo development remains largely unclear. Here we use rAPOBEC1-XTEN-Cas9n-UGI (BE3) to efficiently introduce a point mutation (R17H) into 11 out of 12 loci of multiple copied Hist1/2H3 by a single sgRNA and a premature-stop codon into the catalytic domain of CARM1 in mouse embryos, resulting in the remarkable downregulation of H3R17 methylation levels. Both strategies resulted in developmental defects in pre-implantation embryos and fetal stages with smaller or developmentally delayed embryos. Transcriptomic analysis reveals that Yap1 and cell cycle signaling pathways are dysregulated in Carm1 truncation and H3R17H substitution embryos, and Yap1 overexpression could rescue the base-editing-elicited developmental defects. Our results establish the direct regulatory relationship between CARM1-mediated site-specific histone modification and mouse embryo development, and we also demonstrate that Yap1 acts downstream of CARM1-mediated H3R17me2a to regulate the embryonic development and size determination.