Protein Discovery Tied To DNA Master Switch

The new molecule may prove critical to the regulation of gene expression. If so, it could eventually lead to new treatments for diseases and provide information vital to research aimed at using stem cells to generate organs.

The discovery of the new molecule, SET7, was headed by Dr. Yi Zhang, assistant professor of biochemistry at UNC-CH School of Medicine and a member of the UNC Lineberger Comprehensive Cancer Center. A report of the research is published in the December 21 issue of the journal Molecular Cell.

All gene expression must be tightly controlled, Zhang said. "When we talk about genes, we're talking about DNA in the cell nucleus that's complexed with several basic proteins called histones. The basic structure is like 'beads on a string' which can be further packaged into a high order structure called chromatin," he explained.

"This chromatin packaging allows for efficient storage of genetic information. But it also impedes access to DNA by transcription factors, proteins that regulate gene expression."

Zhang and his colleagues believe their discovery to be part of the mechanism that dynamically changes the chromatin structure, its loosening or tightening. They focused their attention on a particular covalent modification -- methylation, addition of a methyl group to lysine, one of the amino acids that comprise the tail domain of the histone molecules.

Why lysine? Because recent research had linked gene silencing, or deactivation, to methylation of a particular lysine site (lysine 9) on the tail of the histone H3.

As it turns out, modifications of amino acids by methylation mainly occur on lysine. "We've known for three decades that histone can be methylated, but nobody knew the identity of the enzymes responsible for this modification until a year ago when the first lysine 9-specific histone methyltransferase was identified," Zhang said. "The new enzyme we identified, SET7, specifically modifies lysine 4, a different residue on the histone H3 N-terminal tail. It's the first protein ever identified from higher eukaryotes [including all mammals] that methylates histone H3 at lysine 4."

"By methylating H3-lysine 4, SET7 makes the chromatin structure more open, so other proteins can access the gene." The study team also determined that methylation of histone H3 at lysine 4 and lysine 9 inhibit each other. Thus, the findings suggest that methylation of either lysine 4 or 9 could determine gene activation or silencing.

Still, the situation is more complex than that. Among the possibilities, SET7 could have functioning partners yet to be identified. "We know the enzyme modifies lysine 4. After it's modified, we don't know exactly how the gene turns on," Zhang said. Study co-author Dr. Christoph Borchers, assistant professor of biochemistry at the medical school, used mass spectrometry to help identify the protein by measuring the atomic masses of its fragments.

Zhang is currently studying the possible importance of SET7 in embryogenesis, development at the very beginnings of life.

The research was supported with funds from the National Institute of General Medicine at NIH and the American Cancer Society. Zhang's UNC co-authors along with Borchers are Dr. Hengbin Wang; Ru Cao, doctoral student; Li Xia, technician. Drs. Hdiye Erdjument-Bromage and Paul Tempest were co-authors from Memorial Sloan Kettering Cancer Center in New York.