Novel Enzyme Offers New Look At Gene Regulation

In the study, the authors showed that a protein called JHDM1A is able to remove a methyl group from histone H3, one of four histone proteins bound to all genes. Until just last year, the addition of a methyl group to a histone had been regarded as irreversible.

"That histones can become methylated has been known for over three decades, and just now we're learning that those methyl groups can also be removed," said Dr. Yi Zhang, the lead author.

Zhang is professor of biochemistry and biophysics at UNC's School of Medicine and the university's first Howard Hughes Medical Institute investigator. He also is a member of the UNC Lineberger Comprehensive Cancer Center.

The new study is now online in the journal Nature.

"Human genes are so tightly compact within the nucleus that if the DNA of a single cell were unwound and stretched, it would be a line of about two meters in length," said Zhang. "Histones are necessary to package the DNA so that it fits inside a cell's nucleus."

Because they are so intimately associated with DNA, even slight chemical alterations of histones can have profound effects on nearby genes. Depending on the precise location and how many methyl groups are added, their presence can either switch affected genes on or off.

The first enzyme to remove methyl groups from histones, or histone demethylase, was identified last year. This was a breakthrough in the study of histone modifications, but Zhang thought pieces of the puzzle were still missing.

"We hypothesized that there were more demethylase enzymes out there for two reasons," Zhang said. "For one, the previous demethylase identified, called LSD1, could not remove a chain of three methyl groups from a histone, or a trimethyl group. Secondly, common baker's yeast does not have LSD1, although it does have proteins adding methyl groups to histones."

Zhang devised a biochemical strategy to isolate proteins that could remove methyl from histones inside a test tube. The result was the identification of a novel protein, JHDM1A, named for JmjC histone demethylase 1A. A similar protein exists in baker's yeast and has the potential to remove trimethyl groups.

JmjC is only a section of the entire JHDM1A protein, but is required for its demethylase activity. The authors showed that disruption of JmjC prevents JHDM1A from removing histone methyl groups.

Importantly, the JmjC section of JHDM1A, or "JmjC domain," can be found in other proteins, even when the proteins share little else in common. Database searches predict more than 100 total proteins found in organisms as diverse as bacteria and man contain the JmjC domain. This suggests that many other proteins may act similarly to methyl groups from histones or other proteins.

The implications of the new findings are as diverse as the proteins that contain a JmjC domain. For example, hair loss occurs in individuals with mutations in the JmjC domain of a protein called "hairless," possibly due to defects in the appropriate removal of histone methyl groups.

"Given the large numbers of JmjC domain-containing proteins that exist in diverse organisms ranging from yeast to human, our discovery will keep many people in the field busy for the years to come," said Zhang.

Contributing to the work were Drs. Yu-ichi Tsukada and Jia Fang, two postdoctoral scientists in Zhang's lab. Other collaborators include research associate Dr. Maria Warren and assistant professor Dr. Christoph Borchers, both of UNC's department of biochemistry and biophysics, as well as Dr. Hediye Erdjument-Bromage and Dr. Paul Tempst from the Memorial Sloan-Kettering Cancer Center.

The work was supported by funding from the Howard Hughes Medical Institute and a grant from the National Institutes of Health.