If I could remember what thread it was that made mention of how proteins would vary, depending upon other genes being present, or not, I still wouldn't be up for the "prize", since it wasn't my research in the first place. But-- "contradictory examples" as you put it, have been brought out, not as per coding itself, but as to result.
That, I do remember. Just not exactly how, though if memory serves, it involves subtle enough differences in the proteins which result, to have escaped notice for a long while. Beyond transcription being simply turned "on" or "off".
But nevermind that for now,
getting back to this present article of discussion;
I found the webpage at the Rice lab to be very well put together. Good information, put together in a clear and concise manner.
Did you closely examine the illustrations and renderings? That part that ran down the right side of the page was almost as interesting as the ones to the left...
"The complexed histones are encircled by DNA, shown as light gray strands".
It is not the genes that code for the specific proteins themselves, that induce either, which combination of acetylation, methylation, and phosphorylation, occurs in the octameric complex, now is it?
That points to other portions of coding. Which demonstrates overlapping "code". Otherwise, how does the chemical composition of the complex vary, and conversly, is controlled through natural cell processes?
From the abstract;
It beginning to look here, like a case of differing definitions and word usage, at least in part.
Overall, there certainly does appear to be, code within code --- or to put it another way, overlapping code resulting in interactions that convey information.