Turning Genes Off And On: Methylation Process Is Transient, Cyclical And Dynamic, Not Static As Previously Thought

Until the research reported in two papers published in the journal Nature, it had been presumed that in the chemical process of methylation (when a gene is turned on or turned off) a gene was stable and unchangeable. However, arising from the findings of this research group at the European Molecular Biology Laboratory in Heidelberg in Germany which included Dr. George Reid, EMBL Professor in Heidelberg, it has been shown that this is not the case and that the methylation process is transient, cyclical and dynamic. This insight came from an approach of synchronising all cells in a population such that variations were made visible.

With the sequencing of the human genome the general public has become very aware that the answer to many diseases lies in our DNA. Crucially, only some of the total possibility of genes are expressed in any given tissue. For example, a protein that is active in a nerve cell is not expressed in the liver. The way in which this is controlled is a complex area that has attracted much research.

One fundamental controlling factor is whether the DNA is tagged or modified in the region of a particular gene. This modification (methylation) is important not only in gene expression but also in ensuring that there is the right balance in the level of expression of proteins in different cells. For instance women with two chromosomes have one of these silenced by the same methylation tag such that they have one active X chromosome as have men. The consequences of an excess level of expression is well know, for instance in Downs Syndrome where an extra chromosome is active.

One paper shows that this is a general phenomenon occurring at many different genes and in many different cell types. The second paper arises predominantly from the work of Raphael Metivier, a former Post Doctoral student of Professor Gannon, carried out in Rennes in France, which shows a mechanism for this newly described phenomenon.

In the first paper, researchers report that estrogen causes rapid epigenetic changes in breast cancer cells. The new findings impact upon our understanding of how cells interpret their DNA and suggest that epigenetic regulation can affect gene expression immediately and long-term.

Epigenetic changes to the structure of chromatin -- tightly packaged DNA - grant or deny access to the molecular machinery that transcribes DNA and thereby regulate gene expression. One of these mechanisms is DNA methylation, where a small chemical residue called a methyl group is added to strategic bases on the DNA. The methyl group prevents the transcription machinery from docking and thereby shuts down gene expression.

They found out that methylation marks occur rapidly in breast cancer cells in response to hormones such as estrogen or drug compounds. Estrogen withdrawal or treatment with the established anticancer drug doxorubicin cause the methyl groups to be removed from regulatory regions of specific genes within tens of minutes in human breast cancer cells. The treatment sets off a whole cycle of events: initial demethylation renders silent genes active and subsequent remethylation shuts them down again. This cycle repeats itself every 1.5 hours.

"We observed that unlike assumed for a long time methylation can act on a very short timescale. The results challenge our understanding of epigenetics as a means to regulate gene expression permanently," says Sara Kangaspeska, who carried out the research together with Brenda Stride.

"In particular breast cancer is affected by estrogen signalling and changes in epigenetic control," says George Reid, co-senior author of the study. "Our next step will be to find small molecules that target the cyclical methylation processes to elucidate their precise role."

The two papers were published in Nature, 6 March 2008.

1. Transient Cyclical Methylation of Promoter DNA paper was authored by S. Kangaspeska, B. Stride, R. Métivier, M. Polycarpou-Schwarz, D. Ibberson, R.P. Carmouche, V. Benes, F. Gannon & G. Reid. This work was supported by the EC 6th framework programme grant CRESCENDO and by the European Molecular Biology Organisation (EMBO).

2. Cyclical DNA Methylation of a Transcriptionally Active Promoter paper was authored by Raphael Metivier, Rozenn Gallais, Christophe Tiffoche, Christine Le Peron, Renata Z. Jurkowska, Richard P. Carmouche, David Ibberson, Peter Barath, Florence Demay, George Reid, Vladimir Benes, Albert Jeltsch, Frank Gannon & Gilles Salbert. This work was supported by funds from the Ministere de l’Education Nationale de l’Enseignement Superieur et de la Recherche (MENESR), the Centre National de la Recherche Scientifique (CNRS), the University of Rennes, the Association pour la Recherche contre le Cancer (ARC), the Ligue contre le Cancer, and by funding from EMBO and EMBL.