Whereas the possibility that non-coding DNA is functional has been a topic of discussion for decades, it recently has come to the fore with the availability of several sequenced genomes which allow signs of function to be detected at the DNA level. The multi-million-dollar ENCODE project is the largest initiative focused on identifying functional elements in the human genome, but many smaller projects are also ongoing in other species such as mice, Drosophila, and other eukaryotes (e.g., Siepel et al. 2005).
For the most part, the way that potentially functional elements are highlighted is by finding regions of the genome that are essentially unchanged among species whose lineages have been separated for very long periods of time. No change in the sequences suggests that they have been preserved in their present state by natural selection — that is, individuals with mutations in these regions were less fit, and only those with no such changes have left an unbroken line of descendants to the present day. A recent analysis by Katzman et al. (2007) in Science indicated that indeed these “ultraconserved” regions are “ultraselected” in the human genome. Because natural selection is the result of differential survival and reproduction due to heritable phenotypic differences, this provides strong evidence that these regions have some important effect — in fact, probably a function — on the organisms carrying them.
It is important to note that elements exhibiting signs of selective constraint make up a small fraction of the total genome of organisms like mammals, on the order of 5%. Ultraconserved elements in particular represent a very tiny portion of the total DNA. It would therefore be a major exaggeration to assume that the demonstration of such sequences implies that all non-coding DNA is functional. Most or all of it might serve a function, but there is no evidence to support this notion at present. It is also inaccurate to suggest that the discovery of some function in non-coding DNA is a total surprise. Even the early proponents of the “selfish DNA” view of non-coding DNA evolution proposed that some elements would end up being functional, most notably in gene regulation. This certainly appears to have been borne out, and it is quite plausible that more than just the ultraconserved elements are involved in the regulation of coding genes.
However, amidst this backdrop of increasingly refined tabulations of conserved elements in animal genomes there are some observations that raise doubts about just how important they are for organismal fitness. In 2004, for example, Marcelo Nóbrega and colleagues put the importance of conserved non-coding DNA to the test — by deleting some of it. Specifically, they removed two fragments of conserved DNA totaling 1,511 kilobases and 845kb in mice and observed the consequences. Or, more accurately, the lack of consequences. In their experiment, the deletion of more than 2 million base pairs of conserved DNA from the mouse genome had no identifiable effects on the development, physiology, or reproduction of the subjects.
Of course, the mice were kept in lab conditions, and it was argued by some that this may be an unrealistic test given that conditions in the wild are much harsher and any detriment to growth or survival may be hidden in the lab.
In the September 2007 issue of the open access journal PLoS Biology, Nadav Ahituv and coworkers report on a similar but more telling experiment, again using deletions of ultraconserved DNA elements in mice. In this case, the authors deleted four elements ranging in length from 222 to 731bp in ultraconserved regions that are invariant among humans, mice, and rats. More importantly, these regions are known to be located in close proximity to genes for which loss of function mutations result in severe abnormalities.
The assumption, therefore, was that if these regions are conserved because they regulate nearby genes, then their removal should disrupt gene function and result in inviable mice. What did they find?
Nothing. No effect whatsoever was detectable in terms of growth, morphology, reproduction, metabolism, or longevity when any of the four elements was deleted. Again, it is possible that some deleterious effect would show up in the wild, or that there is redundancy that allows other elements to regulate these genes if need be, but as far as the expected phenotypic consequences of disrupting the nearby genes goes, it makes no difference whether these specific conserved sequences are present or not.
At the moment, there is no conclusive evidence one way or another as to the function of most non-coding DNA. It bears noting, however, that although it is very difficult to demonstrate that so much non-coding DNA is non-functional (as this is roughly akin to proving a universal negative), there are reasons to adopt this as the default hypothesis. For example, several mechanisms are known that can generate large amounts of non-coding DNA independent of organismal functions. On the other hand, the evidence for function is thus far restricted to a few percent of the genome, and even here it appears that some of these elements can be eliminated without obvious consequences.
This is not to say that non-coding DNA has no effect; it clearly influences cell size and cell division rate, for example. It is, however, far outstripping the available evidence, and contradicting much of what is already known about genome evolution, to argue that comparative genomics is revealing functions for non-coding DNA at large. At most, genomic analysis is showing genome form, function, and evolution to be much too complex to support any inflexible assumptions on either side.
Ahituv, N. et al. (2007). Deletion of ultraconserved elements yields viable mice. PLoS Biology 5(9): e234.
ENCODE Project Consortium (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
Gross, L. (2007). Are “ultraconserved” genetic elements really indispensable?. PLoS Biology 5(9): e23.
Katzman, S. et al. (2007). Human genome ultraconserved elements are ultraselected. Science 317: 915.
Nobrega, M.A. et al. (2004). Megabase deletions of gene deserts result in viable mice. Nature 431: 988-993.
Siepal, A. et al. (2005). Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research 15: 1034-1050.
Larry Moran has a nice piece on this at Sandwalk. There is also a post about it at This Week in Evolution. Kay of Suicyte (great title — he works on apoptosis) has an interesting post as well. And for goodness sake, could someone please go read Chris Harrison’s earlier post on Interrogating Nature so he can’t stop the crank-like self promotion in all the discussion threads? (Just kidding, Chris –it’s a nice post).