According to the NYT [1] it's 'new' basic genetics. Basically all the 'junk' DNA isn't junk, and the reason the function of that DNA was not appreciated before the ENCODE effort is that these bits appeared 'far away' from the genes which it turns out they affect.

[1] "There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect." http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-...