Considering the effects of epigenetic changes on the embryonic development through altering the gene expression of pluripotency, trophectoderm, and imprinting genes, we determined the pattern of epigenetic alterations in transgenic embryos produced by injecting transgenic mESCs into the morula. To aim this, RAG1 knock-out mESCs were produced using CRISPR-Cas9 editing system and then microinjected into morulas to develop chimeric embryos. Afterward, the expression of pluripotency, trophectoderm genes, and imprinting genes in these embryos were evaluated using real-time PCR. Immunohistochemical analysis was carried out to determine the methylation rates of H3K9me3 and H3K4me3. In the following, since epigenetic alterations can be at least one of the possible reasons of male infertility and the loss of germ-line transmission capacity, the germ-line transmission ability in chimeric mice was also evaluated by breeding them and subsequent backcrosses to wild type strains. Our findings showed that the methylation rates of H3K4me3 and H3K9me3 were significantly lower and higher respectively in the RAG1 knock-out embryos compared others groups. Moreover, the chimeric embryos exhibited the decreased expression of NANOG, OCT4, CDX2, TEAD4, and H19 genes. Following the breeding of chimeric males with normal female mouse, 40% of chimeras had no germ-line transmission (GLT), and 60% were infertile.We showed that the manipulation of mESC by CRISPR-Cas9 approach remarkably changed the methylation status of H3K9me3 and H3K4me3, resulting in impaired development of embryos through dysregulation of genes involved embryonic development and then, may be one of the reasons of infertility and lack of GLT.