There has been a lot of discussion regarding discoveries in genomics, in terms of both genes (especially their number) and non-coding DNA (in particular whether any of it is functional and how much of it is transcribed). All of this supposedly contradicts long-held assumptions about genomes, especially those attributed to the early proponents of “junk DNA” or “selfish DNA” such as that all non-coding elements must be totally non-functional.
I thought I would share some quotes about this topic that I found interesting.
The observation that up to 25% of the genome of fetal mice is transcribed into rapidly labeled RNA, despite the fact that probably less than half this much of the genome serves a useful function, indicates that much of the junk DNA must be transcribed. It is thus not too surprising that much of this is rapidly broken down within the nucleus. There are several possible reasons why it is transcribed: (1) it may serve some unknown, obscure purpose; (2) it may play a role in gene regulation; or (3) the promoters which allow its transcription may remain sufficiently intact to allow RNA transcription long after the structural genes have become degenerate. 
These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA. 
The observations on a number of structural gene loci of man, mice and other organisms revealed that each locus has a 10-5 per generation probability of sustaining a deleterious mutation. It then follows that the moment we acquire 105 gene loci, the overall deleterious mutation rate per generation becomes 1.0 which appears to represent an unbearably heavy genetic load. Taking into consideration the fact that deleterious mutations can be dominant or recessive, the total number of gene loci of man has been estimated to be about 3×104. 
The creation of every new gene must have been accompanied by many other redundant copies joining the ranks of silent DNA base sequences, and these silent DNA base sequences may now be serving the useful but negative function of spacing those which have succeeded. 
It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another. 
It seems that what the new publications do, rather than overturning any previous claims, is indicate that some authors don’t read the literature that they cite.
Part of the Quotes of interest series.
1. Comings, D.E. 1972. The structure and function of chromatin. Advances in Human Genetics 3: 237-431.
2. Ohno, S. 1972. So much “junk” DNA in our genome. In Evolution of Genetic Systems (ed. H.H. Smith), pp. 366-370. Gordon and Breach, New York.
3. Orgel, L.E. and F.H.C. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607.