A team of researchers, including biologists at Washington University in St. Louis, has discovered the key role one protein plays in a major turn-off -in this case, the turning off of thousands of nearly identical genes in a hybrid plant.
Studying the phenomenon of nucleolar dominance, in which one parental set of ribosomal genes in a hybrid is silenced, Craig Pikaard, Ph.D., Washington University professor of biology in Arts & Sciences and colleagues have identified the protein HDA6 as an important player in the silencing. Using the experimental plant genus Arabidopsis, they have shown that HDA6 is located in the nucleus of Arabidopsis cells, and they have imaged it, characterized it biochemically and defined its role in two cellular activities that help bring about gene silencing.
According to Pikaard, genes can be turned off when acetyl groups - little two-carbon entities - are removed from histones, the proteins that wrap the DNA, and when methylation -- a chemical modification of cytosine, one of the four chemical subunits of DNA -- occurs. The removal of acetyl groups is called deacetylation. He and his collaborators found that one of many predicted histone deacetylases in Arabidopsis, HDA6 is a key player in both histone deacetylation and DNA methylation of ribosomal RNA genes. Both types of modification are studied as part of a biological field known as epigenetics, the goal of which is to understand how the packaging of DNA and its associated proteins can affect gene expression. In plants, as well as animals, some epigenetic traits are stable and can be inherited when a cell divides or even into the next generation.
Pikaard explains that understanding how some genes are selectively silenced and how silenced alleles can be turned on again may someday have practical benefits. For instance, tumor suppressor genes that normally help keep cells from dividing uncontrollably are often silenced by DNA methylation and histone modifications in cancer cells, contributing to tumor growth. And certain blood disorders resulting from defective genes expressed in adults might be alleviated if versions of those same genes that are only expressed very early in development, but are then silenced in adults, could only be turned on again. Though only dreams, at present, these sorts of ideas add to the excitement surrounding the field of epigenetics.
For many years biologists thought that gene silencing in nucleolar dominance was a result of one set of ribosomal RNA genes being selectively turned on. But in 1997, Pikaard and colleagues found that they could switch on the silent genes using chemicals that inhibit either DNA methylation or histone deacetylation, indicating that turning off one parental set of ribosomal genes was really the secret to nucleolar dominance. In other words, all the factors needed for expression of the genes were in place but somehow the silenced genes were denied access to them. Since that time, Pikaard and his colleagues have been on the hunt for the proteins responsible for keeping the silenced genes off.
In their current paper, published on-line on April 28, 2006, in Genes and Development, and the cover story for the print version of the journal due out May 15, Pikaard and his collaborators describe a systematic effort to examine the 16 predicted histone deacetylases in the genome to see if any play a role in nucleolar dominance. They made transgenic hybrids in which each of the deacetylases were knocked out one by one and then examined the plants to see if there were effects on nucleolar dominance. In this process they found that knocking down HDA6 eliminated nucleolar dominance, such that the normally silent genes were now turned on.
To find out where HDA6 is located in the cell, the group then genetically engineered the protein to include a fluorescent tag and found that much of the HDA6, seen as a glowing red signal under the microscope, shows up in the nucleolus, which is precisely the site where ribosomal RNA genes are regulated and where nucleolar dominance occurs. "We found HDA6 at the scene of the crime, which was reassuring," Pikaard said.