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03/27/2003
Expression. Part 2
Last week we discussed the subject of “gene expression”, the
process by which the portion of the four-letter code in a double
helix of DNA corresponding to a gene is transcribed onto an
RNA molecule. The human genome project has come up with
the startling finding that, contrary to the earlier belief that our
genome contained perhaps 100,000 genes, it actually only
contains in the neighborhood of 30,000–38,000 genes. We’re
not as complicated as we thought! And we only have 2-3 times
as many genes as the roundworm and the fruit fly. Even so,
we’re still complex enough, to my way of thinking.
We ended last week’s column with a question left unanswered,
namely, how does a heart cell know it’s a heart cell? Put another
way, with all those 30,000 or so genes in every cell in our body,
how does a heart cell know which genes to express to make the
proteins needed for the heart to function? We can ask the same
question about the liver, muscle, skin and all the various types of
cells in our bodies.
To recall and expand a bit on last week’s material, let’s look
again at DNA. The two strands of DNA, entwined together in
the famed double helix, are held together by the bonds between
the bases designated by the letters A, T, C and G. These bases
are not very complicated. For example, the A (adenine)
molecule consists of just 5 atoms each of carbon, hydrogen and
nitrogen (C5H5N5). As we said last week, A only bonds to T
and C only bonds to G. The A-T and C-G bonds are actually
what are known as “hydrogen bonds”. In the chemical world,
hydrogen bonds are rather weak bonds, much weaker, for
example, than the bonds between carbon atoms in diamond.
We all drink zillions of hydrogen bonds every day. Water is
loaded with them. A hydrogen from a water molecule not only
bonds strongly to its own oxygen in the H2O molecule, but can
also form a weak hydrogen bond to the oxygen in a neighboring
molecule of water. Hydrogen bonds can also form between
hydrogen and nitrogen, and both types of hydrogen bonds are
present in DNA. Why do I mention this? It’s the relatively weak
hydrogen bonding of the two ribbons of DNA in the double helix
that allows the ribbons to be opened up and permit the
polymerase to get in there, read the A-T, C-G code and form the
messenger RNA. Thus the hydrogen bonding plays a role in
gene expression.
If the bonding is so weak, how come the polymerase doesn’t go
in and read the whole shebang of genes on a strand of DNA?
That’s a big question and it looks as though we might have some
clues as to the answer. Last week we noted that the DNA in the
cell nucleus is wrapped around little spools of so-called “histone”
proteins? With a six-foot plus strand of DNA double helix, there
are lots of little spools of histones around which the DNA is
wrapped and the result resembles a string of beads. Actually, in
the cell nucleus, the string of beads is coiled up to fit into the tiny
space available in the nucleus.
We gave a hint last week as to what determines whether a given
gene is expressed, that is, is opened up to the polymerase to do
its decoding job. Specifically, we said that the accessibility of a
gene to the polymerase depends on how tightly the portion of
DNA containing the gene is wrapped around the histone spool.
If it’s wound too tight, the polymerase can’t worm its way into
the DNA to read the gene’s code. This sounds like a neat
explanation. In a heart cell, certain genes are loosely wound and
get expressed, while the rest are tightly wound and remain
“silent”. All well and good, you say, but how do the heart cell
DNA strands get wound loosely and tightly in the right places?
Enter “histone tails”. These are chemical hook-like projections
that extend out from the ends of each little histone spool. The
spools hook together in the chromosome somewhat like a Lego
set. The tightness or looseness of the DNA wound around the
histone spool is determined by the chemistry of the tails. This
may be an oversimplification. The nature of the tails may simply
determine how tightly or loosely the histone spools are packed
together. Either tight winding or close packing of the spools
would make it difficult for the polymerase to get into the DNA, it
seems to me.
It now appears that we not only have a DNA code, but we also
have a “histone code” that is itself a fundamental factor in
allowing us to live and develop as we do. This histone code, the
chemical nature of the various histone tails, is presumably passed
along to successive generations of cells of the same type along
with the DNA code. The histone code will determine which
genes are active and which are silent. In other words, the histone
code determines which cells are heart cells and which are skin
cells. If this is true, the histone code ranks right up there with the
DNA code in importance.
This was my impression as of last week. However, on the
Rockefeller University Web site, I found mention of some
histone tail work in Robert Roeder’s laboratory there that makes
the role of histone tails even more crucial. The work, reported in
the April 2002 issue of Molecular Cell, showed that the histone
tails do not act only as a tightening-of-DNA agent but also play a
key role in the gene expression itself.
Among the Rockefeller experiments was one in which they
removed the tails from the histone. The natural assumption was
that removing the tails would take away the factor causing the
tightening or close packing of the gene. This in turn would allow
the gene to “open up” and be expressed. To their surprise, the
gene was not turned on but remained silent. The conclusion is
that the tail is not just a suppressor of gene activity but also plays
a role itself in the activation of the gene. It also seems logical to
conclude that something else, perhaps in the histone spool, keeps
the gene from being expressed.
The Rockefeller group also did some experiments with a couple
of proteins that were found to activate, help to open up, the
particular gene they were studying. One of these proteins, called
p300, is involved in a chemical reaction called “acetylation”. I
won’t go into the chemistry, but earlier work had suggested that
acetylation of the tails plays a role in opening up the gene. In the
Rockefeller experiments, they left the tails on the histone spools
but modified the tails so they could not be acetylated by the
p300. Sure enough, the gene remained silent, showing that
acetylated tails are indeed necessary for that gene to express
itself.
We’ve alluded to the fact that there are other factors that
influence gene expression. For example, Danny Reinberg and
his colleagues at Robert Wood Johnson Medical School have
found a molecule they call FACT. FACT allows the polymerase
to read the DNA while still spooled on the histone by going in
and removing some of the histone proteins ahead of the
polymerase and then replacing them behind it as it goes along.
(Reinberg, incidentally, was mentored as a postdoc by Roeder,
the head Rockefeller guy.)
I don’t know about you but I’m blown away by the fact we
haven’t even begun to skim the surface of all the amazing
processes that go on in a single cell, which typically is less than a
thousandth of an inch in size. We haven’t even touched upon the
fact that a gene encoding for a given protein may also produce a
couple different proteins! How is this possible with just one
DNA and one histone code? Can there be more than one histone
code for the same gene? I haven’t mentioned “interfering RNA”
(RNAi); or the enzyme Dicer, which chops up RNA to form
small bits of interfering RNA. Just last year, workers found that
these small bits of RNAi can shut down genes permanently.
They may also interfere with messenger RNA before it can carry
out its mission. This effectively silences a gene even when it’s
been expressed! Gene expression is not a simple subject.
For me, delving into the inner workings of our cells has been
quite rewarding, and quite challenging. Black holes and the Big
Bang seem relatively simple subjects compared to what goes on
inside our bodies.
Allen F. Bortrum
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