GMW: Salvage prospect for 'junk' DNA

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GMW: Salvage prospect for 'junk' DNA

" GM WATCH " <info

Wed, 26 Apr 2006 13:38:50 +0100

 

 

 

 

GM WATCH daily

http://www.gmwatch.org

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As Craig Venter - leader of one of the team's that decoded the human

genome - memorably remarked, " We don't know sh*t about biology. "

 

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Salvage prospect for 'junk' DNA

By Paul Rincon

BBC News science reporter

BBC NEWS, 26 April 2006

http://news.bbc.co.uk/1/hi/sci/tech/4940654.stm

 

A mathematical analysis of the human genome suggests that so-called

" junk DNA " might not be so useless after all.

 

The term junk DNA refers to those portions of the genome which appear

to have no specific purpose.

 

But a team from IBM has identified patterns, or " motifs " , that were

found both in the junk areas of the genome and those which coded for

proteins.

 

The presence of the motifs in junk DNA suggests these portions of the

genome may have an important functional role.

 

The findings are reported in Proceedings of the National Academy of

Sciences journal.

 

But they will have to be verified by experimenters in the lab, the

scientists behind the work point out.

 

Dr Andrew McCallion, who was not an author on the new paper, commented:

" Up until not so long ago, we were under the impression that the vast

majority of information in the genome, if not all of it, was encoded in

those stretches of DNA that encoded proteins.

 

" We now understand there is much more complexity involved, " Dr

McCallion, from the McKusick-Nathans Institute of Genetic Medicine at

the Johns

Hopkins University School of Medicine in Baltimore, US, told the BBC

News website.

 

Lead author Isidore Rigoutsos and colleagues from IBM's Thomas J Watson

Research Center used a mathematical tool known as pattern discovery to

tease out patterns in the genome.

 

This technique is often used to mine useful information from very large

repositories of data in the worlds of business and science.

 

Scrapheap challenge

 

They sifted through the approximate total of six billion letters in the

non-coding regions of the human genome and looked for repeating

sequence fragments, or motifs.

 

" One of the things that arises from this paper is that junk DNA may not

be junk. But this needs to be verified, " Dr Rigoutsos told the BBC News

website.

 

The researchers found millions of the motifs in non-coding DNA. But

roughly 128,000 of these also occurred in the coding region of the

genome.

These were also over-represented in genes which are involved in

specific biological processes.

 

These processes include the regulation of transcription - the beginning

of the process that ultimately leads to the translation of the genetic

code into a peptide or protein - and communication between cells.

 

Dr Rigoutsos said his team's work suggested, " a connection between a

vast area of the genome we didn't think was functional with the part of

the genome we knew was functional " .

 

He explained that experimental work would be needed to establish this

connection: " The average lab does not have the resources to prove or

disprove this, so it will need a lot of effort by lots of people, " he

explained.

 

Gene silencing

 

The paper in PNAS suggests that the actual positioning of the motifs is

associated with small RNA molecules that are involved with a process

called post-transcriptional gene silencing (PTGS).

 

" A human embryo starts out as a single fertilised cell and rapidly

divides into a widely complex series of cells that become a human being, "

explained Dr McCallion.

 

" Every cell in that human being contains the same complement of genes

and what makes each cell different is the precise way that genes are

turned on and turned off. "

 

PTGS turns genes off after the process of transcription has taken

place. One way in which this occurs is through " RNA interference " , which

involves the introduction of double-stranded RNA molecules.

 

These trigger the degradation of another type of RNA molecule known as

messenger RNA (mRNA), " down-regulating " the gene. During transcription,

this molecule encodes and carries information from genes to sites of

protein synthesis.

 

" These regions may indeed contain structure that we haven't seen

before, " said Dr Rigoutsos.

 

" If indeed one of them corresponds to an active element that is

involved in some kind of process, then the extent of cell process

regulation

that actually takes place is way beyond anything we have seen in the

last decade. "

 

Paul.Rincon-INTERNET

....

[side table]

The double-stranded DNA molecule is held together by chemical

components called bases - Adenine (A) bonds with thymine (T); cytosine

© bonds with guanine (G)

 

These letters form the " code of life " . There are estimated to be about

2.9 billion base-pairs in the human genome wound into 24 distinct

bundles, or chromosomes

 

Written in the DNA are 20-25,000 genes, which human cells use as

starting templates to make proteins. These sophisticated molecules

build and maintain our bodies

 

 

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