From Scientific American:
There’s more to your DNA than your DNA. We are now becoming aware of the epigenome. While DNA controls you, your epigenome may help control your DNA, or rather, it can have an extensive impact on how your DNA is expressed. The epigenome consists of changes in the structure of your DNA, how it is packaged, what parts of it are available for expression into RNA and proteins. For example, adding methyls to DNA tends to decrease the gene expression of that DNA segment, while taking away methyl groups increases it. The cool thing about epigenetics is that the methylation can vary from tissue to tissue, controlling how different genes are expressed in say, liver vs spleen.
Take muscle tissue for instance. Gene expression in muscle tissue can change the efficiency of glucose metabolism by muscle. And glucose metabolism has a very large effect on many bodily processes, include weight gain and problems like cardiovascular disease and type II diabetes. Muscle itself is very plastic, and responds quickly to changes in the environment (which for a muscle, means increases and decreases in exercise or how many calories are getting in). We know that exercise can change gene expression in muscle, but can it also change the epigenome? While immediate changes in gene expression can be very short, changes to the epigenome indicate much longer-term changes. Could bouts of exercise influence the methylation of muscle, and thus have long-term effects?