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Gene Deserts, shifting sands

Started by manofsan , Dec 09 2004 08:19 PM

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#1 manofsan

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Posted 09 December 2004 - 08:19 PM


Here is an article on the gene deserts (aka "junk DNA"), and their role in gene regulation

http://www.scienceda...41208231423.htm

Statistics are the indirect empirical tool being used to survey these gene deserts for useful regulatory finds.

But what is the more direct way to determine epigenetic/regulatory capability of a section of non-coding DNA?
Is there any kind of more direct computational method?

We already know about Folding@Home, but is there any Epi@Home or Junk@Home, that can more firmly assess the epigenetic characteristics of a DNA region using brute force first-principles quantitative calculation?

How can you model the epigenetic characteristics, or regulatory ability of some junk DNA?

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Posted 09 December 2004 - 11:15 PM

Same as protein folding but with far simpler and more computationally easily derived rules since the DNA molecule has a more limited range of conformational possibilities. What is not known, however, is how to translate all the various structural possibilities into regulatory meaningful information as yet.

What is needed is to extend from the sequence coding information (nucleotide) that is presently available and searchable (using tools such as BLAST) to the ability to extract 3D conformation data that would correlate with regulatory regions whose sequence does not have meaning in raw sequence form but has meaning when extrapolated into a 3D conformation. Not particularly difficult using today's technology and a potential IP goldmine for those that are able to deduce regulatory function first.
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