Function of 80% of the Human Genome Charted

ananyo writes "In what is likely to be a historic moment in science, ENCODE, the Encyclopedia of DNA Elements, has published 30 papers in Nature, Genome Research and Genome Biology today, assigning some sort of function to roughly 80% of the genome, including more than 70,000 'promoter' regions — the sites, just upstream of genes, where proteins bind to control gene expression — and nearly 400,000 'enhancer' regions that regulate expression of distant genes. The project was designed to pick up where the Human Genome Project left off. Although that massive effort revealed the blueprint of human biology, it quickly became clear that the instruction manual for reading the blueprint was sketchy at best. Researchers could identify in its 3 billion letters many of the regions that code for proteins, but those make up little more than 1% of the genome, contained in around 20,000 genes. ENCODE, which started in 2003, aims to catalog the 'functional' DNA sequences between genes, learn when and in which cells they are active and trace their effects on how the genome is packaged, regulated and read. Nature has set up an ENCODE site with an explorer, that groups the papers by topic, and collects all the papers, which are available free."

Comments

Most of it is control code

[bill_mcgonigle]

Just happened to hear an NPR interview on the way back to the office. The researcher described most of the 80% as regulating the expression of the protein codes. Brace yourself Slashdot: he called it the 'operating system'.

Re:Most of it is control code

[fm6]

Yep, and the OS can get reprogrammed by viruses.

Various fields borrow terminology from each other. Not that big a deal. My toaster has a "cancel" button. An old-fashioned "eject" would make more sense to me, but I guess mechanical terminology is less familiar to most people.

Re:Most of it is control code

[tlhIngan]

Yep, and the OS can get reprogrammed by viruses.

It's also got fairly good licensing terms - I mean the OS can be replicated (it is billions of times - once for ever cell), and the OS can make copies of itself (mitosis), and even end up altering itself through random changes (mutations).

A virus only infects one cell to duplicate itself - all the other uninfected cells have their own copy. The antivirus system basically works by killing infected cells.

So all in all, an interesting OS - security worse than Windows (i.e., none at all - just random strings of genetic code can alter the OS - you don't neve need root! just physical access!), yet it really works by sheer number of copies.

Wait for the lawsuits

[viperidaenz]

Wait for the lawsuits when they come across a gene some company holds a patent for. They "invented" it you know.

Re:Wait for the lawsuits

[whydavid]

This is probably the single-most important factor in determining whether or not we'll see "personalized medicine" within the next 50 years. The fact that a company owns a patent on the idea of testing the BRCA1 and BRCA2 genes for breast cancer susceptibility is absurd.

When we understand how this works

[anubi]

The sky will be the limit.

The understanding of how DNA works, ( and correspondingly, how to hack it ) is the ultimate reverse-engineering accomplishment.

Life is a textbook, full of worked examples. We are at the stage we realize there is an alphabet, the letters mean something, and have the definition of a few words. Kindergarten stuff.

If we play our cards right, and don't spend all our resources fighting amongst ourselves, the future is incredibly bright. We have worked examples of damn near everything we need... photosynthesis ( solar powered CO2 sequestration and energy storage ) for starters. We have bioluminescence, electric eels, and all sorts of sensor examples.

I figure we have been given a huge shipment of arduinos with all sorts of accessories, and we have now figured out how to make the light blink.

We don't know how its wired yet, how the compiler works, and just now figuring out some of what makes the hardware work.

If our society will value knowledge above greed and accounting, if there is anything limiting our potential, I have yet to see it. However if greed and accounting is all we know, we will soon run into all sorts of limits, imposed only by our inability to adapt. First of these will be exhaustion of the earth's fossil fuels, followed by food and water famines. We will be like the chick that hatched, but failed to scratch, find food, and thrive, living off the energy stored in the egg - until it is depleted.

The earth is our egg.

I value highly the knowledge our species acquires. It is our survival.

Re:Junk DNA?

[robotkid]

Am I misinterpreting this, or is the usual belief that many genes are obsolete sequences that have no current function being called into question?

I don't think any serious molecular biologist ever thought the majority of DNA had no function, just as no neuroscientist ever believed that we only use 10% of our brain, but that's precisely the sort of sound bite that, when uttered in a press release somewhere, echos around the public consciousness forever and never dies because it provides a conveniently sciency premise for the next batch of rebooted superhero origin stories. The distinction is that before this study, we knew non-coding DNA was involved in regulation but not to what extent; i.e. there were plenty of specific anecdotal findings but nothing this systematic and large scale.

As for the significance of this sort of work, yes, it exactly like release day for a major software package, it's an anticipatory excitement and not a "we finally found the Higgs Boson after decades of searching" type of achievement. Molecular biologists and geneticists everywhere can now do a simple web search see how this affects the system they are working on without needing to perpetually beg the labs that possess the specialized high-throughput instrumentation to do a one-off experiment just for their favorite gene. . .