Mover and shaker of the genome

Beyond genetics, there is epigenetics, elusive mover and shaker of the human genome – the poltergeist in the machine, no less.

Epigenetics is beginning to explain things that classical and molecular genetics could not. Genetic pathologist Professor David Ravine, professor of medical genetics at the University of Western Australia, says that, almost overnight, epigenetics has become a major new theme running through the biosciences, particularly human health research.

Ravine believes medical research is witnessing the dawn of a revolution comparable to the one that grew out of advances in recombinant DNA technology 25 years ago.

“The Human Genome Project gave us a catalogue of all genes in 2003, and we now know what a few of them do,” Ravine says.

“We are now able to move on and ask questions about what turns genes on and off, and regulates their activity.”

Ravine says epigenetics’ main role is in making adjustments to chromatin – the complex of DNA supercoiled around “spools” of histone proteins, that gives condensed chromosomes their compact structure. Chemical changes to histone proteins prompt chromatin remodelling, which plays a major regulatory role in gene expression.

Epigenetics is also regulated by chemical modifications to DNA. DNA can become methylated, a process in which enzymes attach methyl groups to C-G nucleotides. DNA methylation may “silence” genes by preventing the access of gene-transcription complexes.

The net effect of these changes is to regulate access of the transcription machinery to specific genomic sequences. Inaccessible genes are silent whereas accessible genes are transcribed.

“But epigenetic regulation is more than this,” Ravine says. “The rate of gene expression from the underlying genomic sequence is also influenced by microRNA and other non-coding regulatory RNAs that also act to expose or hide genes from the transcription machinery.

“Epigenetics is already providing a whole raft of new insights into the causes of disease, and with those insights will come new opportunities to test for epigenetic abnormalities in patients whose genes appear normal.

“We now know that virtually all malignancies are associated with multiple methylation abnormalities. Two mechanisms are involved – very often, cancerous cells will exhibit global hypermethylation, or specific tumour-suppressor genes will be selectively methylated, abolishing gene expression.

“Assaying for both these types of methylation defects is likely to lead to improvements in the diagnosis and treatment of cancer.”

---PB--- Histone modification

Major tumour-suppressor genes like P53, the Guardian of the Genome, are mutated in up to 60 per cent of cancers, and Ravine says it is becoming apparent that methylation has silenced tumour suppressor genes in many different types of cancer, including breast and colorectal cancer.

“Chemical agents able to block methylation, like azacytidine, have the potential to reactivate aberrantly silenced genes,” he says. “Although significantly toxic, DNA methylation inhibitors, which can reactive tumour suppressor genes, are already proving to be effective in the treatment of elderly, high-risk myelodysplastic syndrome patients.

“There is also an important class of epigenetic-targeting drugs that can restore gene function by the chemical modification of histones, most notably the action of histone deacetylase (HDAC) inhibitors, which can restore gene function as a result of raised acetylated histone levels.

“Many more of these kinds of drugs are likely to become available in future, because there are many already in the drug-development pipeline. The US Food and Drug Administration has already approved two of them for bone-marrow cancers.”

Ravine says HDACs and demethylating agents tend to act globally, potentially altering normal patterns of histone acetylation and demethylation in healthy cells. The challenge at this stage is to confine their activity to cancerous tissues.

Environmental factors can also change normal methylation patterns. Beckwith-Weidemann syndrome, a rare disorder in the general population, occurs at a significantly higher rate among children conceived by in-vitro fertilisation, although at a rate that is still less than one per cent among these children.

Virtually all the IVF-associated cases occur as a result of a specific epigenetic disturbance that involves the demethylation of an imprinted growth-factor gene, which is normally suppressed during embryonic growth. Over-activity of this gene causes foetal overgrowth, and babies are born with enlarged organs, including a large tongue. Those affected also have a more than 800-fold increase risk of embryonic cancers.

“Epigenetic-based testing has become an important part of the clinical assessment of these cases, as it is for an increasing number of other disorders,” Ravine says. He predicts that screening for epigenetic lesions will soon become as common as conventional genetic screens.

“There are a load of new technologies for determining the methylation status of genes. The most useful of these currently is a method called bisulphate sequencing, that precisely measures the methylation status of cytosine residues in genes. This method is now used wordwide, although it is still not widely known that it was invented by Susan Clark at the Garvan Institute in Sydney.”

---PB--- Rett syndrome

Ravine’s personal research interest is focused on Rett syndrome and autism. Rett syndrome is a serious neurodevelopmental disorder affecting mostly girls, which has both clinical and biological overlaps with autism. Increasingly it is becoming apparent that these parallel overlaps are yielding valuable insights into the nature of autism, which is far more common than Rett syndrome.

“At the level of brain function, both disorders are characterised by impaired neuronal plasticity,” he says.

“Most cases of Rett syndrome arise from mutations within the MECP2 gene, on the X-chromosome, which encodes MeCP2, a methyl-binding protein that participates in the “cross-talk” between DNA methylation and histone acetylation levels. MeCP2 is therefore an important part of the epigenetic machinery.

“Curiously, although it is girls that are mostly affected, Rett syndrome nearly always occurs as a result of a mutation within the MECP2 gene on the paternally derived X chromosome. This parent-of-origin effect indicates that an epigenetic disturbance is contributing to the occurrence of Rett syndrome, although we still do not know what it is.”

His research team within the Western Australian Institute for Medical Research has recently discovered that MeCP2 plays a role in the normal functioning of microtubules. As microtubules within nerve cells are important for the maintenance of neuronal plasticity, Ravine’s team together with collaborators in Sydney are working to characterise the mechanism underlying MeCP2’s action on microtubules. “Surprising, our studies of MeCP2’s role maintaining the function of the microtubule cytoskeleton, are being aided by recent epigenetic advances.”

Ravine’s group is increasingly hopeful that that these insights will enable the discovery of compounds, including epigenetic-targeting drugs, that can cross the blood-brain barrier and ameliorate the serious brain functional deficits associated with Rett and autism.