Epigenetics is the study of heritable genetic information that does not involve changes in the nucleotide sequence of DNA, but, is manifested as chemical marks that are added to either DNA or chromatin proteins following replication. Examples of these marks are DNA methylation and histone modifications such as acetylation and methylation (causing chromatin remodeling). These marks are part of the complex regulatory system that control gene expression and that, along with siRNA and the proteins that initiate transcription, are called transcription factors.
The sum of the epigenetic marks in a genome is called the epigenome and their pattern within a genome is variable between cell, tissue and organism types as they are responsible for controlling gene transcription and silencing.
In humans and most other eukaryotes, cell differentiation and mammalian embryonic development is epigenetic. The approximately 30,000 genes in the human genome are found in all cells but are expressed in different tissues and organs depending on their regulation by different sets and combinations of transcription factors.
During mammalian embryonic development, a process called gene imprinting takes place in which genes on the unused X chromosome, and others involved in differentiation according to sex, are turned "off". Epigenetic marks, specifically DNA methylation, are responsible for imprinting but must be reversed in germ cells during fertilization in order for the zygote to have a complete set of heritable, and expressible, genes. Imprinting is then restored during determination of the sex of the new embryo. Stem cell research has been aided by the study of how imprinting is reversed as scientists determine ways to restore differentiated cells to a pluripotent state.