Using an analogy suggested by David A. Sinclair PhD, the genome can be thought of as hardware whereas the epigenome would be the software. The epigenome consists of chemical compounds that have been added to the DNA, as a way to regulate gene expression. While these "tags" are not part of the DNA sequence itself, they can remain when a cell divides and in some cases, they can even be inherited.
A common way to refer to this process is the addition of "tags", which are methyl groups (CH3), to the genome. When this happens, genes can be silenced. In other words, DNA methylation won't allow a protein to be produced, which can lead to genetic disorders.
In human DNA, methyl groups most often attach at 'CpG sites' (places where a cytosine precedes a guanine in the DNA). A typical human genome contains more than 28 million such sites. But the microarray technology used to detect methylation samples finds only a fraction of them: older machines pin down just 27,000 sites and newer ones around 485,000. (Gibbs, 2014)
As cells age, the pattern of epigenetic alterations shifts, and some of the changes seem to mark time. To determine a person's age, Steve Horvath explores data for hundreds of positions on DNA and notes how often those positions are methylated. He has discovered an algorithm, based on the methylation status of a set of these genomic positions, that provides a remarkably accurate age estimate. (Gibbs, 2014)
The clock's median error was 3.6 years, but accuracy improves to 2.7 years for saliva alone, 1.9 years for certain types of white blood cell and 1.5 years for the brain cortex.
"Because methylation is usually reversible, it might be possible to grab the minute hand of the epigenetic clock and retard its incessant progress". Said Wei Guo at Zymo Research, a biotechnology company in Irvine, California.