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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