Here’s a very interesting quote, provided by Faye Flam at Knight Science Journalism.
I decided … I would go back to ENCODE biologist John Stamatoyannopoulos, who was quoted in the first wave of news. He said he thought the skeptics hadn’t fully understood the papers, and that some of the activity measured in their tests does involve human genes and contributes something to our human physiology. He did admit that the press conference mislead people by claiming that 80% of our genome was essential and useful. He puts that number at 40%. Otherwise he stands by all the ENCODE claims:
“What the ENCODE papers (not the main paper in Nature, but the other length papers that accompanied it) have to say about transposons is incredibly interesting. Essentially, large numbers of these elements come alive in an incredibly cell-specific fashion, and this activity is closely synchronized with cohorts of nearby regulatory DNA regions that are not in transposons, and with the activity of the genes that those regulatory elements control. All of which points squarely to the conclusion that such transposons have been co-opted for the regulation of human genes — that they have become regulatory DNA. This is the rule, not the exception….”
Some co-option of TEs has been known for a long time, and was fully expected by the authors of the “selfish DNA” papers in 1980. 40% of the genome functional in this manner, though? We shall see. Correlation is not causation, and TEs being active under different circumstances can be explained in various ways. In any case, even John Stamatoyannopoulos is now backtracking on the 80% claim, stating that the evidence is consistent with the view that the majority of the genome does not, in fact, have any functional role in the way that word is usually understood.