Re: Get your New Junk here!

On 14 Jun, 17:30, "Perplexed in Peoria" <jimmene...@xxxxxxxxxxxxx>
wrote:
"Ernest Major" <{$t...@xxxxxxxxxxxxxxxxx> wrote in messagenews:hxM$0WU2KVcGFwVV@xxxxxxxxxxxxxxxx

<snip>

You can find the relevant papers at

http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html

and

http://www.genome.org/content/vol17/issue6/

Thx to Glenn and Ernest Major for the links. It is going to take a
while to assimilate all this stuff, but it does appear that this is
potentially 'paradigm-shifting' new information. It is possible that
some of the defenders of the old "Most 'junk' really IS junk!" viewpoint
may have to eat our words.

The most dramatic new info is mentioned in the quote above:

... the discovery that the
majority of DNA in the human genome is transcribed into functional
molecules, called RNA, ...

The shock is that a 'majority' is transcribed - the usual estimates up
until now have been that only about 5% is transcribed. But I am a bit
puzzled as I read the Nature paper. I find the statement
To begin with, our studies show that 14.7% of the bases represented
in the unbiased tiling arrays are transcribed in at least one tissue
sample.
But I don't see how that 14.7% becomes "the majority". Can anyone point
out what I am missing?

I looked at Supplementary Table 4 in S2.5.3 of Supplementary
Information 1.

The 14.7% figure appears to be due to the exclusion of introns. The
techniques for assaying RNA may be quick, but they aren't quick enough
to get a look before the introns are gone.

The 14.7% figure also seems to be the union of the results of physical
experiments (the TxFrag/RACE) and the results of pencil and paper
checking of published genomes (the GENCODE, PET, and CAGE).

I can quite believe "the majority" statement, but I am curious how the
sample they physically looked at (interrogated), comes to be so heavy
on coding genes in the first place - introns may be big, but shouldn't
they be rare compared to junk?

<snip>

.

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