Unraveling DNA: Genetic Collaboration in Genomes?

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New research shows that the human genome is much more complex than once thought.

Image: ABC News.

A study was published this week in the journal Nature, revealing that genomes are more complex than previously thought. These studies, which analyzed just 1% of human genome, or DNA code, challenges the view that genes are the primary players in biochemistry. Instead, so-called "junk DNA" and other regions appear to collaborate with each other to form a network that controls gene expression and cell physiology.

ENCODE, short for The Encyclopedia of DNA Elements, is an international collaboration between 80 different laboratories and research institutions, investigating the function of DNA sequence data generated by the Human Genome Project. The human genome is composed of 24 distinct chromosomes (22 autosomes plus two sex chromosomes; X and Y), made up of approximately 22,000 genes and intergenic "junk DNA" regions comprising a total of approximately 3 billion DNA base pairs (see below).

The "coding DNA" comprises only 3% of the total DNA while the other 97% or so is made up of so-called "junk DNA". "Junk DNA" was so named because it originally had no known biological function. However, the study found that "junk DNA" was being actively transcribed, or copied, into RNA. RNA is an active molecule that relays information from the DNA to the cellular machinery that builds proteins. ENCODE found that the "junk DNA," plays a powerful role in how the genome functions.

"The Human Genome Project gave us the letters of the genome, but not a great deal of understanding. The Encode project tries to understand the genome," said Ewan Birney, from the European Molecular Biology Laboratory's European Bioinformatics Institute, who led ENCODE's analysis efforts.

Another key aspect of this research was that so many scientists worked together harmoniously to complete this important study.

The researchers studied only 1% of the human genome, carrying out 80 different types of experiments that generated more than 600 million data points.

"We are now seeing the majority of the rest of the genome is active to some extent," observed Tim Hubbard from the Wellcome Trust Sanger Institute. "This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed," he added.

This study begins to answer a fundamental question that scientists have been asking for a while: How do cells in the body operate differently when they all have exactly the same DNA?

"What we've known for a long time ... is that every cell in the body has the same DNA, but every cell uses different genes, and that's what defined them," said John Greally of the Albert Einstein College of Medicine, who reviewed the study.

This study heralds a new direction in the study of DNA and genomes because it is unveiling broader implications for how DNA drives cellular physiology as well as differences between individuals and between species, whose genes are often similar.

"As we understand these things better, we get better insight into disease, and when we get better insight into disease, we get better insight into diagnosis and the chances to create new drugs," said Birney.

The researchers are planning to broaden their efforts to look at the other 99% of the genome.

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BBC News (quotes)

ABC News (quotes, top image)

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In Genetics, 98.7% of the human DNA used to be considered (by some) "Junk". The rest, 1.3% were the "Genes".

This era is gone, forever, and the field is leveled. There are two immediate questions:

1) What is the new science after discarding a dogma?
2) What is the algorithm of Genome Regulation?

PostGenetics (http://www.postgenetics.org) is "Genomics beyond Genes".

An algorithmic approach to the whole genome is FractoGene (http://www.fractogene.com); that fractal DNA governs development of fractal organelles, organs and organisms.

pellionisz_at_junkdna.com

Another key aspect of this research was that so many scientists worked together harmoniously to complete this important study.

Although curiously, only about 10% of them actually did anything. The rest seemed to just sit around, without any apparent function. Further research is required to discover whether these so-called "junk scientists" actively contribute to the project, or whether they are just selfish elements, which hang around in the lab drinking coffee, and reading email.

Bob

Well, to be fair to to the term "junk DNA", it was originally meant to describe only those portions of DNA which we know have no purpose (which do still exist), but was fairly quickly coopted into describing all noncoding DNA. Even in the 70's, there were researchers stating that calling something junk DNA did not necessarily mean that it had no purpose, just that we didn't know what it did.

Unfortunately, it is a term which is so easily misunderstood that the wrong interpretation (that all junk DNA has no purpose) is the one most often attributed to it.

By CaptainBooshi (not verified) on 14 Jun 2007 #permalink

"Although curiously, only about 10% of them actually did anything. The rest seemed to just sit around, without any apparent function. Further research is required to discover whether these so-called "junk scientists" actively contribute to the project, or whether they are just selfish elements, which hang around in the lab drinking coffee, and reading email.

Bob"

Hilarious. Best thing I've read this month. It seems that these 'junk scientists' provide a sort of warehouse for natural selection - they have function but provide no adaptive advantages for the study. However, in the future, they may gain enough mutations (or "publications") to eventually become adaptive.

That fact that segments of DNA are important for gene expression regulation is not a new idea. Small interfering RNA were discovered as non-protein coding RNA's a while back. I think the important thing in this "landmark" publication is HOW MUCH of the "junk DNA" is involved in regulation.

If anyone is curious, Omnome published a post on this subject last week.
http://omnomescience.blogspot.com/2007/06/what-did-encode-decode.html

Just a thought....I read a description of DNA that left me with this image...DNA is not a blueprint, it is more like a recipe box. It has all the codes so that a cell can make whatever it needs... The cell goes to the recipe box and gets the needed recipe.

I think science should take a hint from the scientists who are changing the terminology used for parts of the avian brain. Words do have power, and if we label something as primitive, for example, we may discourage study of that thing by encouraging preconceived notions of worthlessness. Using cute buzzwords like "junk" can be fun, but it can be more detrimental to progress as it may deter people from studying (or agencies from funding study of) "junk".

Clapping

Chardyspal

By Chardyspal (not verified) on 23 Jun 2007 #permalink