Clipped from "The Human Genome: RNA Machine:"
The evidence for large numbers of ncRNAs and for the central importance of ncRNAs as regulators of important developmental, physiological, and neural processes is compelling.14 If all these ncRNAs are functional, as the evidence increasingly suggests they may be, then much and perhaps most of the human genome is functional. If so, the genetic programming of the higher organisms has been fundamentally misunderstood for the past 50 years, because of the presumption - largely true in prokaryotes, but not in complex eukaryotes - that most genetic information is expressed as, and transacted by, proteins.
And almost all the mutations we see leading to defects are in either genetic regions or regulatory regions.
Regions that can express ncRNAs may be counted as regulatory - IF we can find what they are regulating and how - and figure out why mutations seem to not change its function.
http://blog.openhelix.eu/?p=103
It promotes the idea, erroneous, that there are two kinds of DNA, coding and junk, functional and non-functional.
As I found out in my own Ph.D. studies, the “non-protein-coding” DNA is quite diverse. I studied retrotransposable elements. I have to admit, I’m a former-adaptionist when it came to retroposons. I had a difficult time at first grasping that such a huge part of the genome had no function, for the organism. After more study and thought, I came to the conclusion that retroposons were “selfish” elements having, as a class, no intrinsic function in the genome, but are rather parasitic. Did this make them “junk,”? No, not in the original coined meaning, and not particularly how it’s used now. Are they “non-coding”? No, they code for reverse transcriptase and other proteins. Are they non-functional? Yes and no. They are non-functional like a tick might be for me, but pretty functional when it comes to the tick’s existence.
There are also a lot of sequences in the genome that are ‘throwoffs,’ pseudogenes and the like. DNA that has no function for the genome or for themselves, that could be considered like the ‘junk’ I throw in the basement of my house. I haven’t used it in years, it once might have have a function, it doesn’t now. That I might go back into my basement some day and find a new function for it (as I’ve done recently), doesn’t mean that it now has an intrinsic function, still junk.
And of course there is a lot of DNA, like perhaps these ncRNAs, that have a function in the genome that hasn’t been determine yet. I think what we are finding, and have found, is that the classes of DNA in our genome are quite diverse, protein-coding, regulatory, scaffolding, parasitic, purely unnecessary throw off junk and so much more. I am sure we are going to find functions for DNA sequences we hadn’t ascribed before. 20,000 some protein coding genes need a lot of help to make an organism as complex as a mouse or human. That said, there is a hell of a lot of sequence that is there that we can show to have no ‘function’ in the genome.