In 1823 there was a fire in the basilica, and when they built a new one, they simply filled St. Paul’s crypt with earth and put an altar on top of it. St. Paul, the father of the Roman Catholic Church. (Well, there are a few fathers I guess. This is the Paul who wrote part of the New Testament, not the Paul how was one of the 12 disciples)
EDIT: Oops, Paul isn't one of the 12 disciples. Hahaha, I am ignant.