'Junk' DNA reveals vital role II
Pooua
mentioned the last time is about to present new results of his
studies:
"Gill Bejerano, PhD, assistant professor of developmental biology and
of computer science at Stanford, found more than 10,000 nearly
identical genetic snippets dotting the human chromosomes. Many of
those snippets were located in gene-free chromosomal expanses once
described by geneticists as 'gene deserts.' These sections are, in
fact, so clogged with useful DNA bits - including the ones Bejerano
and his colleagues describe - that they've been renamed 'regulatory
jungles.'
"'It's funny how quickly the field is now evolving,' Bejerano said.
His work picking out these snippets and describing why they might
exist will be published in the April 23 advance online issue of the
Proceedings of the National Academy of Sciences.
"It turns out that most of the segments described in the research
paper cluster near genes that play a carefully orchestrated role
during an animal's first few weeks after conception. Bejerano and his
colleagues think that these sequences help in the intricate
choreography of when and where those genes flip on as the animal lays
out its body plan.
"In particular, the group found the sequences to be especially
abundant near genes that help cells stick together. These genes play a
crucial role early in an animal's life, helping cells migrate to the
correct location or form into organs and tissues of the correct
shape."
(Full article at link)
http://www.terradaily.com/reports/Junk_DNA_Now_Looks_Like_Powerful_Regulator_999.html
John Harshman
> Following up on a post I made on 11 May 2004, the same researcher I
> mentioned the last time is about to present new results of his
> studies:
>
> "Gill Bejerano, PhD, assistant professor of developmental biology and
> of computer science at Stanford, found more than 10,000 nearly
> identical genetic snippets dotting the human chromosomes. Many of
> those snippets were located in gene-free chromosomal expanses once
> described by geneticists as 'gene deserts.' These sections are, in
> fact, so clogged with useful DNA bits - including the ones Bejerano
> and his colleagues describe - that they've been renamed 'regulatory
> jungles.'
>
> "'It's funny how quickly the field is now evolving,' Bejerano said.
> His work picking out these snippets and describing why they might
> exist will be published in the April 23 advance online issue of the
> Proceedings of the National Academy of Sciences.
>
> "It turns out that most of the segments described in the research
> paper cluster near genes that play a carefully orchestrated role
> during an animal's first few weeks after conception. Bejerano and his
> colleagues think that these sequences help in the intricate
> choreography of when and where those genes flip on as the animal lays
> out its body plan.
I will be most interested to find out about these snippets that
simultaneously occur in gene deserts and cluster near genes. Quite a trick.
Tell me: are these snippets conserved among species? If so, they
wouldn't have been considered junk to begin with.
r norman
A search of the PNAS website produces no hits for author Bejerano. A
full search produces a relatively large number of papers where he is
cited in the bibliography, all the papers dealing with non-coding
conserved elements.
His web site (although apparently an older one) says: "My research
focuses on the "dark matter" of the human genome. These are genomic
regions, highly conserved between human and other organisms. Most of
these regions have no known function, while others appear to be far
more conserved than their known or conjectured function calls for. I
am particularly interested in the many thousands such elements that
appears to control gene transcription during development."
http://www.soe.ucsc.edu/~jill/
John Harshman
Don't mind me. I'm just complaining about the bizarre language used in
science press releases.
r norman
<jharshman....@pacbell.net> wrote:
I have just about given up responding to people who post press
releases as if they describe real science.
Perplexed in Peoria
"John Harshman" <jharshman....@pacbell.net> wrote in message news:GHoXh.563$RX...@newssvr11.news.prodigy.net...
Yeah. The bit about clustering near genes in the gene-free deserts caught
my attention too. But it may not be as ridiculous as it sounds.
Here is an earlier paper from this group.
http://www.soe.ucsc.edu/~jill/papers/science04.pdf
Here, they also have things in deserts which were close to interesting genes
and which appeared to function as enhancers. It makes a bit more sense when
you see the numbers.
In this paper, the sequences in question are clearly conserved among species,
and hence are not 'junk', by your definition of junk. 'Ultra-conserved' among
species, in fact. But it is interesting that the conservation seems to be
limited to the vertebrates. In many cases, they can't even find homologies
to anything in drosophila, etc. So we are talking about something which
apparently first appeared in vertebrates at about the time of the 'Cambrian
Explosion' and has been conserved by selection ever since. Interesting stuff.
The 'deserts' are themselves something of an interesting phenomenon. They, too,
are conserved in a sense. Not conservation of sequence, but conservation of
absense of coding genes. Probably something that is worth understanding.
Most non-coding DNA clearly is junk. About 95% of the genome, in fact. But
of that remaining 5% that is probably not junk, only about a quarter of it
codes for protein, and perhaps another quarter has known functions (rRNA,
promoters, intron splice signals, etc.) So that means that about half of
the DNA that probably has a conserved sequence-specific function still has
no *known* function. Molecular genetics may look very different a decade
from now.
I've noticed that the press releases for PNAS 'early-release' papers usually
arrive a day or two before the paper itself, so we should be able to read
what the latest hype from Bejerano is all about fairly soon.
Ken Shaw
Well that's that then. Godidit and evilution is the false teaching of
Satan.
Hold on a second though...
These snippets are identifiable because they are so similiar and so
highly conserved. What would make us suspect that highly conserved
snippets of DNA had function? It couldn't possibly be one of the most
basic predictions of the Theory of Evolution could it? What do you
know, more confirmation that the ToE is the best model for the origin
of diversity of living things yet devised.
Ken
derdag
So. Not only does a random accident happen to a gene coding for a
protein in the hair follicle, but another simultaneous regulatory
accident has to happen in the regulatory jungle which directs the
histological interaction of different cell types during stem cell
differentiation at the time of growth and development.
It sure is a good thing that this type of construct is so consistant
and congruent with the ToE. lol