Genes activation, or epigenetics is a rather new known phenomena (modern studies started in the 90s). Basically it's the concept that operation of genes is changed by behavior, but not the DNA itself; A change in phenotype without a change in genotype.
I'm not super versed in this subject.
Usually I think these changes are very specific, much like regular training adaptations.
I know about one study where they had a group of people cycle only on one leg. Only the trained leg showed epigenetics change.
http://www.tandfonline.com/doi/full/10.4161/15592294.2014.982445
So this would appear to show that running a lot would not give you improved tendons, bones and muscles anywhere but in parts used in running.
There is probably more to that, this is only one study. There is a number of diabetes studies showing exercise changes genes body wide in skeletal muscle and adipose tissues, so some changes might be global. Maybe the aerobic component? This is wild speculation. Then again, the exercice in the studies is generaly pretty global too.
So yeah, I cannot really answer definitely.
If you are interested in the subject, there are a lot of relevant references in the article above. However, I believe current knowledge in the matter is at the stage of hypothesis. We know something happens. We know a little what happens. We do not know why or how. We could explain some stuff with it, still need to prove it.
