Epigenetics refers to modifications in gene expression that are controlled by heritable but potentially reversible changes in DNA methylation and/or chromatin structure. DNA methylation is a post-replication process by which cytosine residues in CpG sequences are methylated, forming gene-specific methylation patterns. Housekeeping genes possess CpG-rich islands at the promoter region that are unmethylated in all cell types,  whereas tissue-specific genes are methylated in all tissues except the tissue where the gene is expressed. These methylation patterns obviously correlate with gene expression. Further direct experiments proved that one of the most efficient gene-silencing mechanisms involves DNA methylation. Methylation patterns are established in the embryo by erasure of the gametic methylation patterns in the preimplantation embryo followed by global de novo methylation at the pregastrula stage, leaving CpG islands unmethylated. Finally, specific demethylation shapes the adult gene specific methylation patterns. Once a methylation pattern is established, it is clonally inherited using a maintenance methylasse that copies the methylation pattern on the parental DNA strand to the newly replicating strand. About 1% of the genes do not obey Mendel’s genetic rules being expressed monoallelically in a parent-of-origin fashion. This phenomenon was called genomic imprinting and this subset of genes is imprinted by an epigenetic mechanism. The imprint must be established during gametogenesis, maintained during embryo development and erased in the primordial germ cells to set the stage for establishing a new imprint according to the gender of the embryo.

DNA methylation had been suggested as a suitable candidate to serve as the imprint since it can be established by de novo methylation, erased by demethylation and maintained by maintenence methylation. Methylation, being involved in gene silencing, may also account for the monoallelic expression of the imprinted genes. In fact, all imprinted genes possess differentially methylated regions (DMRs) that may play a role in the imprinting process. To examine this hypothesis, a DMR in the imprinted gene igf2r was studied. This DMR is established in the zygote by methylation of the maternal allele and prevents methylation of the paternal allele. This is controlled by a 113 dp imprinting box that includes in its 3’ end an 8 bp element that is responsible for de novo methylation of the entire DMR and a 6 bp element at 5’ end that discriminates between the alleles by preventing methylation of the paternal allele. The de novo methylation signal (DNS) binds a specific protein factor (DNP) and the allele discrimination signal (ADS) binds another specific protein (ADP). Binding of ADP to the paternal allele presumably interferes with DNP binding to this allele, resulting in an unmethylated status of the DMR on the paternal allele.  This allows synthesis of antisense RNA  from a promoter located  downstream of the imprinting box. The antisense RNA abolishes transcription of the igf2r gene mRNA. The methylated status of the DMR on the maternal allele prevents the synthesis of antisense RNA, and as a result the igf2r mRNA is formed. It has recently been shown than in cloned sheep, the imprinted status of igf2r fails to be reprogrammed since it has not ben passed through the gametes. DMR is consequently unmethylated on both alleles and the gene is completely unexpressed, resulting in large offspring syndrome (LOS). Failure to reprogram the imprinted state of imprinted genes can cause developmental defects, neurological diseases and tumorigenesis, jeopardizing cloning and the recent use of embryonic stem cells to grow tissues in culture for implantation.