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If selection pressure results in conservation of DNA sequences, what is the most plausible explanation for the existence of ultra-conserved elements (refs here and here) given that there hasn't been any significant validation of the functional significance of these elements other than a lot of bioinformatic analyses across different genome datasets? If these are of such high significance, does this mean that there is still some significant gap in our understanding of fundamental biology or is there another explanation? The second reference in particular show that there are UCEs shared between plants and animals, but are not syntenic (which is not necessarily a surprise) so it might suggest that at least a class of UCEs are associated with structural rather than functional elements.

It appears that there are at least several different 'classes' of ultra-conserved elements, based on the number of matching/identical bps, their spatial distribution across the genome and the species in which they exist. Even though there is probably no single explanation that would account for all the possible functions they can have, it is surprising that they are difficult to test functionally. This is again probably due to a lack of understanding about their properties and therefore no real method to validate their function. I think this is where we need to think outside the box to come up with the answer.

What would be the most obvious (and possibly not so obvious) function for UCEs?

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  • $\begingroup$ What is the question? The papers you linked to already talk about the "most obvious" function for them. $\endgroup$ – Superbest May 17 '14 at 10:12
  • $\begingroup$ I am also interested in the not so obvious functions as well. $\endgroup$ – Michael Lai May 17 '14 at 13:33
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Probably development, in particular transcriptional regulation. To quote each link in turn,

They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development.

and

[Highly conserved non-coding sequences] are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments

Additionally,

Here we report that 45% of these sequences functioned reproducibly as tissue-specific enhancers of gene expression at embryonic day 11.5. While directing expression in a broad range of anatomical structures in the embryo, the majority of the 75 enhancers directed expression to various regions of the developing nervous system.

These regions tend to be highly clustered in around 200 areas, and most of them are non-coding. ncRNA is often regulatory, and those UCE clusters are associated closely with developmental genes. That being said, not all of them are clustered near known genic regions, which might be a good indicator that there are heretofore unknown genes in those areas; UCEs might be useful for discovery. And here's a paper trying to give a role to one in cancer.

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  • $\begingroup$ I definitely like to think that it is involved in development or some type of regulatory control. However, if it is unique to vertebrate, then why are they also found (exactly identical) in other branches of life? I think we also have to be conscious that sequence location proximity doesn't necessary indicate its association with particular genes. Unfortunately some of the knockout experiments haven't really provided any definitive answers, but this is a mystery that has definitely proved to be intriguing to say the least. $\endgroup$ – Michael Lai Sep 17 '13 at 22:27
  • $\begingroup$ @MichaelLai Because that study looked at humans and pufferfish; removed enough to draw conclusions about vetebrates but not instructive beyond that. The third link I posted deals with non-vertebrates as well. $\endgroup$ – Amory Sep 17 '13 at 23:05
  • $\begingroup$ This is a good answer about RNA world you should mention it. $\endgroup$ – user1357 May 14 '14 at 6:17
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It's with noting that just because something is evolutionary diverged sequentially through specialization does not mean that that function has not been to the same degree conserved. For instance non coding RNA are not characterized by sequential homology alone but through structural conservation. To a greater degree even this structure function relationship exists in other parts of the genome with retro elements and beyond the genome with proteins especially antibodies.

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  • $\begingroup$ Does this give some hint to what their possible function(s) might be? What are your thoughts about the different types and functions that are possible? $\endgroup$ – Michael Lai May 14 '14 at 22:57
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Conservation might indicate selective pressure as a general rule, but this isn't a given; you can delete some ultraconserved elements and still get viable mice...

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050234

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  • $\begingroup$ Does this also suggest that there are different types of ultraconserved elements? Or that they have a function that is not directly related to structural or signaling? $\endgroup$ – Michael Lai May 14 '14 at 22:54
  • $\begingroup$ It suggests that high-degrees of conservation might itself not imply selective pressures - at least from a proximal perspective the deletion events should have resulted in loss of fitness if the preservation of those elements was under strong selective pressure. $\endgroup$ – Ankur Chakravarthy May 18 '14 at 18:34

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