junk DNA

[Rcjohnsen]

<< Subject: Re: junk DNA
From: iayork at panix.com  (Ian A. York)
Date: Mon, Apr 17, 2000 6:37 PM
Message-id: <8dflm0$c05$1 at news.panix.com>

In article <20000417142406.19749.00001881 at ng-ba1.aol.com>,
Rcjohnsen <rcjohnsen at aol.com> wrote:
>
>The termm 'junk DNA' is an unfortunate coinage of what used to be believed as
>useless DNA, but the alu sequences were derived from a bacterium and may have
>had some role in our rapid evolution from the chimpanzee.

(1)  Alu sequences are only a fraction of "junk" DNA.
(2)  I suspect you're thinking "virus", rather than "bacterium".  If not,
what reference do you have for alu being derived from a bacterium?
(3)  I suspect you are confused between using alu sequences to track
evolution, and alu sequences to drive evolution.  If not, what references
do you have?
 >>
I quote from the article entitled 'Transposons'(not a scientific article) but I
hace science refs. as well
  Transposons
So called junk DNA proves its worth: First in corn, now in creatures like us
by Ayala Ochert
published in Discover Magazine
Dec, 1999, pgs 59-65

They are offering the article free at their site at
http://www.discover.com

    "In fact, Cal Tech molecular biologist Roy Britten, who was one of the 
first to spot transposons in the  genomes of mammals, argues that the movement
of transposons has had a  much more significant effect than  classical
mutations—those in which  a single base change results in a slightly  different
protein. When transposons  jump to new locations, they can alter  patterns of
gene expression, and therefore have far more of an effect on  how an organism
actually turns out.  Britten believes that transposons are  unsurpassed as a
source of natural variation. "You couldn't explain the process  of evolution on
the basis of single point  mutations. You need a more powerful device." That
powerful device, he  says, is the transposon.
Britten has been particularly interested in how a transposon called  the Alu
element could affect patterns  of gene expression. Alus are unique to  primates
and, for some unknown reason, they seem to have  spread widely around 30 
million to 50 million years  ago. Although their period  of intense activity
occurred  long before human-apes  _ ever walked the earth,Alus  have left a
signature in our genome. Each of us has nearly a million Alus, and they make up
more than  five percent of our DNA.  In fact, says Britten, the Alu element  is
the most abundant type of transposon in the human genome. And, according to
molecular biologist Wanda  Reynolds, the Alu may have played a  critical role
in our own evolution.
    When Reynolds began studying  Alu elements at the Sidney Kimmel  Cancer
Center in San Diego several  years ago, she noticed that part of the  Alu
sequence bore an uncanny resemblance to something she had seen  before. She had
been working with  distinctive DNA sequences that act as  anchor points for
proteins that bind  to hormones. When a hormone is  bound in this way, it can
switch on a  whole set of genes, starting a cascade  of biochemical events
throughout the  body. When the hormone estrogen  for example, binds to such a
sequence  it triggers the genes involved in ovulation. Or when growth hormone
binds  to a similar stretch,  it triggers the gene  necessary to make a child
grow.
    These sequences are extremely  powerful, so the discovery that they  reside
in all Alu elements startled  Reynolds. As Alus moved around during primate
evolution, they would  have had the power to alter which set  of genes got
triggered by which hormone and when. She also found that  various Alus bind to
several different  hormones, including retinoic acid,  thyroid hormone, and
even estrogen—all of which are critically important in the timing of
development.
    "These Alus could have generated more diversity—but subtle diversity," says
Reynolds. "We're not talking about knocking a gene out, but just slightly
elevating or reducing its expression in certain tissues, so that you could
gradually change the evolution of the species. Alus were probably very
important in primate evolution, because without them you may never have had the
diversity from which to select the primates " says Reynolds.
    The importance of this subtle diversity becomes clear when you consider the
differences between ourselves and our closest living relatives, the
chimpanzees. Although they share more than 98 percent of our genes, it is less
often acknowledged that such a small distinction can hardly begin to account
for the very real differences between how we and they look and  behave. "It's
not just the sequence of the genes, it must be something about the way genes
are turned on, the way they're controlled," says McDonald. "There must be
different patterns of expression that are key to the differences in morphology"
Wlth their ability to bind hormones and thus switch genes on and off during
development,  Alus may very well have shaped the evolution of our species.
    The more we learn about transposons and their powerful effects, says
McDonald, the harder it becomes to think of them as mere junk. "Before,
everything on the molecular level was considered random. But there's actually
selection going on at the molecular level, driving evolution on the organismic
level. Because these mechanisms are being driven from the inside, that speeds
the whole thing up."