According to a gaggle of papers released today (six in Nature alone), it turns out that this "junk" actually plays a very important regulatory role in controlling how and when the non-junk dna does its job. Or, as an article on Nature puts it -
One of the more remarkable findings described in the consortium's 'entrée' paper is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly 'junk DNA'. The authors report that the space between genes is filled with enhancers (regulatory DNA elements), promoters (the sites at which DNA's transcription into RNA is initiated) and numerous previously overlooked regions that encode RNA transcripts that are not translated into proteins but might have regulatory roles.Or, as I would put it, the 2% of our DNA that was thought to be significant is only a small part of the picture. What matters more is whether that small part is turned on or off and when these transitions happen. There doesn't have to be a known mutation in a known gene for a part of the biological processes in a person's body to be messed up. There are many things that can control how genes are turned on or off and today we learned of yet another major one.
There are news articles in all of the major outlets such as the NY Times, The Washington Post, The Wall Street Journal, and Business Week just to name a few. And there is an excellent resource on the Nature site as well.
Time will tell what this means for people with autism but I predict a renewed interest in "junk" genetic mutations associated with autism. Which will be a little bit of a shame, really, since the idea that autism is "genetic" has almost been put out to pasture. First it was mutations are strongly associated with autism, that came up largely empty, then it was copy number variations are strongly associated which was another bust, now it is going to be junk dna causes autism. I think this avenue of investigation is going to be a bust as well but at least it might get people looking at genetic regulatory mechanisms which is where I suspect the problem actually is.
I guess we will have to wait and see what happens.