Junk DNA

The first papers from the ENCODE Project: ENCyclopedia Of DNA Elements came out in Nature and Genome Research this week. The project’s goal is to understand non-coding DNA seqeunces by focusing in on 1% of the genome with multiple experimental approaches.

It’s not getting described well in the press. This news article is quite giddy: link

DNA study challenges basic ideas in genetics
Genome ‘junk’ appears essential

By Colin Nickerson, Globe Staff | June 14, 2007

A massive international study of the human genome has caused scientists to rethink some of the most basic concepts of cellular function. Genes, it turns out, may be relatively minor players in genetic processes that are far more subtle and complicated than previously imagined.

Among the critical findings: A huge amount of DNA long regarded as useless — and dismissively labeled “junk DNA” — now appears to be essential to the regulatory processes that control cells. Also, the regions of DNA lying between genes may be powerful triggers for diseases — and may hold the key for potential cures.

The details are interesting for biologists but not super surprising. Here’s an overview of non-coding DNA:

2% of the human genome encodes proteins. A difficult problem is to figure out what the the remainder, the non-coding DNA, does. About 1% is clearly involved in regulating protein expression, and a few additional percent have other known functions. An additional 2% are conserved non-coding sequences, DNA that has kept its sequence for tens of millions of years. The function of most of these conserved non-coding sequences is not known but their DNA has been retained because it has a function.

While it is hard to prove a negative, most of the remaining 90+% is likely non-functional (’junk DNA’) or very weakly functional. Some bits are likely spacers the sequence of which is unimportant. About 1/2 the human genome is transposons, bits of DNA that have copied themselves over and over (it is like the genomic inbox is full of spam).

The most interesting finding is that some non-coding non-conserved DNA is functional. Exactly how this works biologically is not clear–so very new, very cool. Ultimately, this adds another 1-2% to the functional non-coding class of DNA.

So it is interesting to hear that a new function for a bit of the non-coding DNA has been discovered–there will be a lot of cool new biology working out what bits of this do. Still, most of the genome is junk DNA.

The amount of junk DNA in a genome can vary a lot. There are some frogs and salamanders with genomes ten times larger than humans. These animals likely have about the same number of genes as humans. They are thought to just have a *lot* more junk DNA.

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