Study helps explain gene silencing in developing embryo

CHAPEL HILL – – New research at the University of North Carolina at Chapel Hill sheds light on the process that silences a group of genes in the developing embryo.

Down regulation of gene expression, or gene silencing, is considered crucial in normal development. In the embryo, proteins expressed by different sets of genes help signal the pattern of development, including limb formation. However, when that work is completed, the genes responsible must be turned off, said Dr. Yi Zhang, assistant professor of biochemistry and biophysics at UNC’s School of Medicine and a member of UNC’s Lineberger Comprehensive Cancer Center.

“During the early embryonic development, a group of genes called Hox genes needs to be expressed. After they’ve been expressed and have set the body pattern, they have to be silenced permanently during the life of the organism,” Zhang said.

Zhang said another gene group known as the Polycomb group has been intensely studied for its role in silencing Hox in organisms as diverse as flies and mammals, including humans. “We know that if something is wrong with the Polycomb group, if these genes are mutated and cannot silence Hox, then development becomes abnormal.”

Writing in Friday’s (Nov. 1) issue of Science, Zhang and co-authors from UNC, Southern Methodist University and Memorial Sloan-Kettering Cancer Center report the purification and characterization of a Polycomb group protein complex. Their research has established a link between Polycomb gene silencing and histone protein methylation, the addition of a methyl group to lysine, one of the amino acids that make up the tail region of histone molecules.

Four core histone proteins are highly conserved in eukaryotic organisms, those having nucleated cells. These histones are involved in packaging our genetic information: DNA. Each contains a globular domain and an amino terminal “tail.” Of interest to Zhang and others at UNC and beyond is that histones, specifically processes that modify them (including methylation), are thought to play a major role in gene expression and cell division.

“Basically, we found that the Polycomb proteins function through methylating a particular lysine residue, lysine 27, on histone 3,” Zhang said. When enzyme activity causing methylation of this site is blocked, Hox gene silencing does not occur.

Given those findings, Zhang and his study team could explain the permanence of Hox gene silencing. “Histone methylation cannot be reversed. It becomes permanent, a long-term genetic marker. Thus far, no ‘histone demethylase’ has been discovered.”

It may well be that methylation and other modifications of histone proteins are part of an emerging “histone code” of modifications that ultimately regulates gene expression. This code was postulated three years ago by Drs. David Allis and Brian Strahl at the University of Virginia. (Strahl is now at UNC.) Currently under investigation by Zhang and colleagues in several UNC departments, a histone code would be in addition to the now familiar genetic code of repeating As, Cs, Gs and Ts of DNA nucleotide sequences.

Through this histone code, differentially modified histone proteins could organize the genome into stretches of active and silent regions. Moreover, these regions would be inherited during cell division.

The study was supported by grants from the National Institute of General Medicine at the National Institutes of Health and the American Cancer Society.