A team led by Craig Pikaard, Ph.D., WUSTL professor of biology in Arts & Sciences, has made a breakthrough in understanding the phenomenon of nucleolar dominance, the silencing of an entire parental set of ribosomal RNA genes in a hybrid plant or animal.
Since the machinery involved in nucleolar dominance is some of the same machinery that can go haywire in diseases such as cancer, Pikaard and his collaborators' research may have important implications for applied medical research.
Nucleolar dominance occurs when nucleoli, protein-rich, dense regions of RNA within the nucleus, form on the chromosomes inherited from one parent, but not on the chromosomes inherited from the other parent. Expression of ribosomal RNA genes drives the formation of these nucleoli. The hybrid, a result of a cross-breeding of two different species, always "chooses" to express the ribosomal RNA genes of one particular parental species, regardless of whether that species happens to be the maternal or paternal parent.
Ribosomal RNAs, or rRNAs, are a major component of the ribosomes, the protein manufacturers of the cell. Because rRNA genes are highly redundant, cells use nucleolar dominance to control the dosage of ribosomes in an organism.
According to Pikaard, if researchers could harness the silencing machinery involved in nucleolar dominance to limit the expression of rRNA genes, they could potentially slow the growth rate of tumor cells and thereby slow the progression of diseases like cancer.
In cancer cells, nucleoli are conspicuously large because of a dramatic increase in the transcription of rRNAs, which in turn leads to an increase in the production of ribosomes. This escalation in ribosome activity means that the cell can synthesize proteins at an alarmingly rapid rate, which contributes to the out-of-control cell proliferation that is the disease's trademark.
Completely silencing all ribosomal genes would not be a viable therapeutic approach for cancer patients because ribosomes are necessary for survival. But Pikaard and his collaborators' research suggests that small interfering RNAs (siRNAs) can direct silencing agendas that are much more sophisticated than an all or nothing approach.
"Dr. Pikaard's study demonstrates the potential of a plant model system to yield important molecular details on how cells silence large clusters of genes," said Anthony Carter, Ph.D., who oversees gene regulation grants at the National Institutes of Health's National Institute of General Medical Sciences, which partially supported the research. "His findings on the control of a major class of RNA found in all cells offer new insights into gene silencing mechanisms."
Pikaard and his collaborators' work, which was published in Molecular Cell on Dec. 4, is also one of the first to demonstrate how siRNAs can play a role in controlling the dosage of vital genes. The research was supported by the National Institutes of Health and the National Science Foundation.
The weird and the wacky
Nucleolar dominance is considered an "epigenetic" phenomenon. Epigenetics refers to heritable changes in gene expression that arise from changes in the "packaging" of DNA rather than modification of the underlying DNA sequence itself. Because these changes do not follow the normal rules of genetics, Pikaard refers to them as the "X-files of biology," unusual events that are not easily explained nor predicted.
Although biologists have been studying nucleolar dominance since the 1920s, this phenomenon remained largely unresolved until recently, when Pikaard's lab reversed an old dogma. Up until this point, researchers had presumed that nucleolar dominance was all about turning on one set of parental ribosomal genes. In 1997, Pikaard and his colleagues made headlines with an experiment that used chemicals to inhibit the two-pronged method cells employ to silence genes -- DNA methylation, which adds chemical flags to genes, and histone modification, which alters the proteins that act as spools for DNA. The chemical inhibitors of silencing turned on the previously unexpressed set of parental genes, thereby demonstrated that the underlying mechanism of nucleolar dominance turns genes off, not on.
Since then, Pikaard and his collaborators have been working to disentangle the complex machinery behind this epigenetic on-off switch.
Using RNA to fight RNA
To determine the pathway regulating nucleolar dominance, Pikaard's team exploited a naturally occurring cellular mechanism known as RNA interference (RNAi).
Pikaard likens RNAi to a "search and destroy mission." Fragments of RNA known as small interfering RNAs (siRNAs) prevent specific genes from being expressed by guiding cleavage of matching RNA strands. Once these RNA strands are cut into smaller pieces, they can no longer be translated into proteins. RNAi has high specificity because the target RNA strand must have a genetic code that is complementary to the siRNA's nucleotide sequence.