Human Genome More Like a Functional Network

bshell writes "An article in science blog says we may have to rethink how genes work. So called "junk DNA" actually appears to be functional. What's more it works in a mysterious way involving multiple overlaps that seems to be connected in some sort of network." From the article: "The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active. The new data indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. "Our perspective of transcription and genes may have to evolve," the researchers state in their Nature paper, noting the network model of the genome "poses some interesting mechanistic questions" that have yet to be answered."

Comments

interesting

[wizardforce]

From the article:

The collaborative study focused on 44 targets, which together cover about 1 percent of the human genome sequence. or about 30 million DNA base pairs. The targets were strategically selected to provide a representative cross section of the entire human genome.

The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another.

actually if I remember correctly, there are 30,000 known genes which produce about 100,000 proteins [a little more than 3 per gene] which span a much larger amount of DNA that actually codes for proteins. genes have been known to code for multiple proteins since the Human genome project was completed. It has also been known that certain non-coding regions of DNA are not useless but in fact code for things like ribozymes etc. The article also talks about non-coding regions acting as a source for new structures. that is to say that the non-coding regions mutate and are selected for or against over time to form new proteins/enzymes etc.

Re:Of course its not junk

[Founder of PostGenet]

The genome is fractal - governing fractal growth of organelles, organs and organisms. Even from a single fractal template (e.g. the algorithm of z=z^2+C) an enormously "complex" pattern, full of self-similar repetitions will develop. The "gene"-parts of the genome determine "fractal templates" of proteins, while the "PostGene"-sequences supply the auxiliary information necessary for iterative hierarchical development (architecture of complex protein structures). This concept/utility (FractoGene) triggered 300+ entries in slashdot in 2002 when an algorithmic approach first challenged the "gene/junk" dogma. The saga (including slashdot reference) is recorded at http://www.junkdna.com/ (as well as on http://www.fractogene.com/ ) Of course it is not junk... "junkDNA" is not a scientific term any more - but an important nickname for "the biggest mistake in the history of molecular biology". pellionisz_at_junkdna.com

Re:error correction

[crashfrog]

I don't think evolution would be very kind to unneeded material.

There's really almost no selection pressure against extra DNA sequences, particularly ones with no associated promoter. One of the proofs of this is the fact that the human genome is comprised more of endogenous retroviruses than actual functional sequences.

Original article here

[Anonymous Coward]

Here

It's the same article, really. The blog just copy and pasted the entire article from the government website.

Re:Hmm...

[plunge]

No one thinks that flight just popped into existence. There are all sorts of useful traits prior to actual full flight that the earliest flyers would have developed: heck, things like feathers pretty clearly evolved long before flight was even remotely possible, and likely for very different reasons than flight. As for the thing itself, there are lots of different adaptions and traits on the way to flight that are all useful: things like decreased weight for sprinting across the ground, and of course brief gliding from tree to tree without actually being able to fly.

Re:I just want to let the record show

[plunge]

"No junk DNA would seem to indicate more of an overall design to the system, no?"

Not really. Exactly how and why DNA keeps or discards various sequences, coding or not, is not something on which design or no design rests: it's a matter of the particulars of how DNA works (and it doesn't, actually, work the quite same way in every creature, which complicates matters even more: some creatures have much more robust ways of catching error than others, for instance).

It's also worth noting that the term "junkDNA" is a bit of a misnomer, and any good discussion of the term in biology generally notes it as such: it's possible that your 110 class basically just, well, sucked. If you do a PubMed search, you'll find this discussion goes back way farther than 97: biologists were noting that even apparently non-coding DNA had usefulness for mapping out genomes even back in the 70s.

Re:junk genes was a junk idea

[Anonymous Coward]

Sorry, but how much real practical effect does "efficient coding" have on survival of the fittest.
The idea of junk DNA was a win for evolution, but its absence is surely a win for intelligent design IMO.

Re:Messy Speghetti Help

[Anonymous Coward]

We are predominantly Perl programmers at least on the European side - http://www.ensembl.org/ is the European based Genome browser (probably a million lines of Perl)... plus most of the http://www.sanger.ac.uk/ Wellcome Trust Sanger Institure data manipulation and presentation is in Perl...

See also http://www.bioperl.org/