Re: Shall we get rid of our junk?

I wouldn't draw general conclusions about this for two reasons.

1) It was not 3% of the mouse genome that was deleted, it was less than
0.1% of the mouse genome (2.3 million out of 2.7 billion bases).
2) The region they deleted was what we call a "gene desert."

On the other hand animals certainly do not need the vast majority
of their DNA. Some species have evolved to have a naturally
high DNA deletion rate. These include the pufferfish, and some
species of bats. In these cases you have living complex
genomes 1/10th the size of a typical mammal. 90% of the genome
looks certainly unnecessary, and it may be as high as 95%.

In a broader sense the junk, though not needed at the *moment*
does serve a purpose. The system needs to be able to tolerate
a bunch of non-functional stuff so that it has the necessary freedom
to evolve new functions. Approximately half of the junk is the
relics of quasi-viral "selfish" DNA (transposons). The other half
is from portions of the genome being duplicated, and then one copy
of the duplication undergoing bit rot, since natural selection only
needs
to preserve one working copy. On rare occassions instead of
bit rot the second copy takes on a new function. If the duplicated
'junk' was deleted too quickly, there would be no opportunity for
new functions to evolve.

whitesickle@xxxxxxx wrote:
> Mice thrive without 'junk DNA'
> 20/10/04. By the DOE Joint Genome Institute
>
> Researchers have deleted 3 per cent of the mouse genome, but the mice
> show no apparent ill effects.
>
> After completing the sequencing of the human genome, a question still
> lingers: is all the non-coding DNA (sometimes called 'junk DNA')
> - which makes up nearly 98 per cent of the genome - required, or is
> some of it potentially disposable?
>
> US researchers have now shown that deleting large swaths of DNA
> sequence shared by mice and humans still generated mice that suffered
> no apparent ills from their genomes being millions of letters lighter.
>
> The findings, by researchers at the US Department of Energy Joint
> Genome Institute (JGI) and Lawrence Berkeley National Laboratory, were
> published in the 21 October 2004 edition of the journal Nature.
>
> "In these studies, we were looking particularly for sequences that
> might not be essential," said Eddy Rubin, Director of the JGI, where
> the work was conducted. "Nonetheless we were surprised, given the
> magnitude of the information being deleted from the genome, by the
> complete lack of impact noted. From our results, it would seem that
> some non-coding sequences may indeed have minimal if any function."
>
> A total of 2.3 million letters of DNA code from the
> 2.7-billion-base-pair mouse genome were deleted. To do this, embryonic
> cells were genetically engineered to contain the newly compact mouse
> genome. Mice were subsequently generated from these stem cells. The
> research team then compared the resulting mice with the abridged genome
> to mice with the full-length version. A variety of features were
> analysed, ranging from viability, growth and longevity to numerous
> other biochemical and molecular features. Despite the researchers'
> efforts to detect differences in the mice with the abridged genome,
> none were found.
>
> The negligible impact of removing these sequences suggests that the
> mammalian genome may not be densely encoded. Similar-sized regions have
> previously been removed from the mouse genome, invariably resulting in
> mice that did not survive, because the missing sequences contained
> important genes and their deletion had severe consequences for the
> animal.
>
> Links
> Nobrega M A, et al. (2004) Megabase deletions of gene deserts result in
> viable mice. Nature 431: 988-93. Abstract
> Eddy Rubin research page
> Adapted from a press release by the DOE Joint Genome Institute


.

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