"Scientists discover double meaning in genetic code" - an interesting article

[TeMPOraL]

Seems like some serious stuff.

Original paper: http://bede.im/Science-2013-Stergachis-1367-72.pdf

News report: http://www.washington.edu/news/2013/12/12/scientists-discover-double-meaning-in-genetic-code/

Discussions (much more interesting than the news report): https://news.ycombinator.com/item?id=6896779, http://www.reddit.com/r/science/comments/1sqj63/scientists_discover_second_code_hiding_in_dna/

Jacek Złydach,
http://temporal.pr0.pl/devblog | http://esejepg.pl | http://hackerspace-krk.pl

TRC - Bringing you tomorrow's solutions yesterday.

[Cory Tobin]

We have known that some transcription factors can bind within exons
for quite a while. Apparently these binding sites are now called
"duons." The part of this which is new is this group, part of the
ENCODE consortium, mapped out where a lot of those duons are located.
And the interesting part is how many there are and how they have
affected the evolution of proteins.

It's a pretty cool study and definitely one of the more interesting
things (IMO) to come out of ENCODE, but Univ of Washington's PR
department is way over-hyping this. Claiming that they "discovered a
second code hiding within DNA" is a bit disingenuous. That honor goes
to Jacob and Monod in the 1960s.

-cory

[Mega [Andreas Stuermer]]

A lot of average people will read that in the media and get that wrong. say "look, you geneticists don't know what you are doing. You're messing up with nature".

To some degree, this might partly be true if one just  copies a human coding site (including exons) into an eukaryotic genome. On the other hand, if negative effects would originate, it would be found in cell culture. And those cells are never released into nature anyway.


I, for my part, have never had to use exons :D

[TeMPOraL]

That's the unfortunate problem with average people and the media, regardless of scientific discipline.

Jacek Złydach,
http://temporal.pr0.pl/devblog | http://esejepg.pl | http://hackerspace-krk.pl

TRC - Bringing you tomorrow's solutions yesterday.

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[Cathal Garvey (Phone)]

I saw recent overhype of the same flavour regarding the ribosomal "on ramp" hypothesis, with journos saying it was "a new layer of the genetic code". Er, no. It's just an interesting and immediately applicable refinement of transcriptional efficiency, mate.

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[Mega [Andreas Stuermer]]

Didn't have time to read it, but may I cite rule16 from http://www.reddit.com/r/science/comments/1sqj63/scientists_discover_second_code_hiding_in_dna/
 

The "double meaning" is simply silly overblown language saying that a sequence of DNA base-pairs might simultaneously be exonal AND regulatory AT THE SAME TIME (in a way that shows a unique pattern of conservation).

Well, even I could have told you that "double function" :P

Here on this list it was mentioned several times that the ribosome binding sites of viral genes are often found in the terminal of the previous coding sites.  Also in the lux genes this occures. Where's our nobel prize? ^^

[Koeng]

When I read the media release, at first I was like "wow!" But then I actually caught onto what they where saying... and then I just did this - http://i.imgur.com/ZRMeE.gif

But then again, it may be beneficial. If you think about it, going over the top on how important something is when talking to the public may get you more funding, which is likely the purpose of the release. So, I guess, in that sense it is doing its job.

Anyway, if you want something even more amazing, here is a DNA with triple function

AGGAGTGATGTAATG

The beginning is the Shine-Dalgarno sequence, (bold) and the beginning of a new gene in bold as well. Then italicized is 2 stop codons for 2 different CDSs! That means this DNA has information for 2 CDSs AND a ribosomal binding site! "Where's my nobel prize?" :)

(For clarification, this sequence came from phiX174, which is known for overlapping DNA sequences. http://www.ncbi.nlm.nih.gov/nuccore/NC_001422.1 )

-Koeng

[Andreas Stuermer]

I'm sure you could also include a -35 promoter element in that :P then it has four meanings. And a restriction site :D

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[Koeng]

We should have a contest of who can put the maximum amount of information in a DNA molecule, with the rule that the genes it uses have to be natural 

[Andreas Stuermer]

:D You mean only the UTR may be modified, from ATG everything on must be original?

Changing codons (for same amino acid) allowed?

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[Koeng]

Yep, but you can change codons to make them like fit into each other, maybe someone would make a program to do it

[Patrik D'haeseleer]

Viruses win - lots of examples of overlapping genes with coding regions in different reading frames. Now *there*'s an impressive trick!

[Meredith L. Patterson]

Talk about biomimicry; a hell of a lot of computer viruses behave similarly, to cram as much functionality as possible into as little space as possible.

Cheers,

--mlp

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[Cathal Garvey (Phone)]

Have thought about it, but I think it's out of our reach for now: viruses can mutate their proteins to fit into one another, but the sort of protein structure/function prediction software you'd need to mimic isn't out there yet. We can only reliably substitute synonymous codons without changing protein peptide sequence, which is far more limited.

[Andreas Stuermer]

X-actly... That would be a nice tool for future applications. On the other hand, one mutation may destroy 2 Proteins then.

That's also one hypothesis why introns are common... If a mutation occurs (statistically each xxxxxx bps) it may hit an intron and change nothing at all. 

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