This one and many more very interesting articles, findings can be found
on the GM Watch web site, <http://www.gmwatch.org>.
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GM Watch:

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@bbc.co.u
...

[side table]

The double-stranded DNA molecule is held together by chemical
components called bases - Adenine (A) bonds with thymine (T); cytosine
(C) 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