Hi Gordon,
Sincere apologies to you and other ListServ members for my long
silence. I got snowed under by a series of unplanned NIH events. I also
got a bit overwhelmed with the volume of traffic on this Listserv -- but it
is all very interesting. Regretfully, due to the unremitting press of other
business, I won't be able to answer further queries after today.
Now to your question: The stuff we have been calling "junk" is all
of the nonconserved DNA in introns (the spacers in the midst of the coding
regions) and in between genes. These regions are littered with repetitive
sequences that appear hundreds or thousands of times in the genome. In the
past, these have largely been considered as "selfish DNA" that is just hard
to get rid of. The most abundant example is the so-called "Alu" sequence,
of which we have about 1.5 million copies. This is a mobile element that
still moves around occasionally (it has even caused the new appearance of
cases of hemophilia by landing in the Factor VIII gene).
When we were able to finally look at the entire human genome
sequence, instead of bits and pieces, something interesting appeared. One
can date the time at which a particular Alu sequence landed in the genome by
how far it has subsequently diverged from the original parental sequence.
Some Alus are only a few million years old. Others are much older. There
is a gradual process of loss (by deletion) as well as the arrival of new
elements by transposition. The surprise is that the older Alu elements are
concentrated in the regions where genes are present at highest density. The
most sensible conclusion is that these Alu elements actually provide some
evolutionary advantage by being located near genes (as opposed to being in
the gene "deserts", where no such selective retention is found). That
doesn't sound so much like junk.
One should not jump from this conclusion, however, to say that every
base pair of the 3.1 million base pairs of the human genome has an important
use. That will certainly not be the case (there are large segments of DNA
that are deleted in some individuals, with no apparently consequence). But
we would be wise not to throw the word "junk" around so loosely in the
future.
For more information on this, see International Human Genome
Sequencing Consortium: "Initial sequencing and analysis of the human
genome", Nature, February 2001.
Regards,
Francis
-----Original Message-----
From: gordon brown [mailto:gbrown@euclid.colorado.edu]
Sent: Thursday, April 04, 2002 10:01 PM
To: Collins, Francis (NHGRI)
Subject: RE: GENETICS
Dr. Collins,
I hope this question is not too vague. (It is far removed from my field.)
I seem to recall having read somewhere that at least some of what has been
considered to be superfluous junk DNA may turn out to have a useful
function. Can you comment on this?
Gordon Brown
Department of Mathematics
University of Colorado
Boulder, CO 80309-0395
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