U.VA. scientists find new piece of gene expression puzzle

Scientists at the University of Virginia Health System have identified another step in the mysterious process of gene regulation — what turns genes on or off, making them cause or suppress disease and other physical developments in humans. As reported in this week’s issue of the scientific journal Nature, a chemical group called ubiquitin has been shown to lie upstream of a switch that seems to control whether a gene is on or off. “Ubiquitin was first discovered on histones long ago, but before this study, we really did not know what it was doing in chromatin,” said lead author and investigator Zu-Wen Sun, senior post-doctoral fellow in the Department of Biochemistry and Molecular Genetics at U.Va. Ubiquitin is one of manydistinct kinds of chemical “flags” that are known to be present on histone proteins.

Histones are protein building blocks around which the DNA is coiled much like a Slinky toy. Together, they form a structure called chromatin, where additional levels of gene regulation occur outside the DNA itself. One mechanism for regulating gene expression in the form of chromatin is through the addition or removal of chemical groups that are attached to the histone proteins. These histone proteins are nearly identical in most complex living organisms, from humans to yeast, which was used as a model in this study. They are highly decorated with different kinds of chemical groups including methyl- and acetyl- groups. Distinct patterns of these marks may operate together to form a ’histone code’ that, in turn, precedes and influences gene activities within the chromatin, according to studies published last year by C. David Allis, Byrd Professor of Biochemistry and Molecular Genetics at U.Va., who is co-author of the new study.

The four major types of histones each have a long “tail” which “wags” outside the surface of the chromatin fiber. Last year’s studies examined lysines at the fourth (K4) and ninth (K9) positions on the tail of one of the histones, H3, and revealed that when a chemical methyl group is added to these two positions, it turns genes on or off, acting much like a master control switch according to a histone code.

The new study found an unexpected mechanism that dictates whether methylation occurs at the K4 position of H3. It showed that another chemical group called ubiquitin, which is attached on the tail of a completely different histone, H2B, affected methylation of lysine at this K4 position on the H3 tail. This phenomenon, referred to as “trans-tail” regulation of the histone’s chemical changes, was unexpected, Sun said, because all other related chemical reactions previously identified, such as methylation of K4 and K9 lysines, occurred in relatively close proximity on the same histone tail.

“It is the first time that the modification on one histone’s tail has been seen to affect what occurs on another histone tail,” he said. “And, in addition, we now understand better how the ubiquitin and the enzyme responsible for adding it to the histone H2B in the first place is linked to gene regulation.”

Sun and Allis said that defects in the ubiquitin pathway in mice already have been generally connected to male infertility. It is possible that the problem could be traced from defects in the addition of the ubiquitin group in chromatin, to defects in the addition of the methyl group, and to subsequent changes in gene expression, which then disturbs proper cell differentiation.

“It means we have to start looking at how the whole group of these histone proteins functions together as a unit, as well as individually,” Allis said. “If the ubiquitin chemical flag seems to govern methylation of lysine at K4, but not elsewhere, there is a selectivity going on, and it’s remarkably more complicated than we thought. When we reported on the methylation of lysine at K4 and K9 last summer, we had no clue it was being regulated by something else as described in our new study. So we would like to find out what is it about ubiquitin that causes such a dramatic influence on histone methylation.

“It’s a new chain reaction for chromatin,” he said. “It is a major new finding in this field with a very old histone modification.”

The study was funded by the National Institutes of Health and the U.Va. Cancer Center.

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