Quite simply, there are more methylated cytosines than normal when a promoter is hypermethylated and less when it is hypomethylated. There is nothing inherently beneficial or negative about either state. Generally more methylation means less transcription of the gene, but even this is not consistent across all genes, or indeed even consistent within different domains of the same promoter. Any observation of differential methylation, while suggestive, is not in itself enough to impute a functional outcome.

Quite simply, there are more methylated cytosines than normal when a promoter is hypermethylated and less when it is hypomethylated. There is nothing inherently beneficial or negative about either state. Generally more methylation means less transcription of the gene, but even this is not consistent across all genes, or indeed even consistent within different domains of the same promoter. Any observation of differential methylation, while suggestive, is not in itself enough to impute a functional outcome.

Thank you Dr Richard

In general (Richard is right when pointing to heterogeneity), methylation of promoters impedes the binding of transcription factors, and in a second stage leads to chromatine condensation, with long term repression of gene expression. What does that mean in terms of "beneficial or detrimental" depends on the cell, the context, the gene etc.

To know more:

http://en.wikipedia.org/wiki/Dna_methylation

And more on epigenetics in general:

http://www.amazon.co.uk/The-Epigenetics-Revolution-Understanding-Inheritance/dp/1848313470

Thank you Dr Nicolas for your explanation- I have one more thing to ask and Whether the methylated status of a particular Promoter/gene can be used to predict the extent of toxicant exposure in a biological system- If so, what could be simplest method to follow ?

I am not sure what you mean by "toxicant exposure in a biological system". But the reaction to a toxic substance most probably depends on the expression of the relevant transporters, receptors and degradation enzymes. Thus, the methylation state of the related genes could be used as a proxy. I am not aware of any statistical studies in that direction, but that would be a fantastic research project!

Thanks a lot Dr. Nicolas. What i mean is, If a particular population in an area is consuming water contaminated with Fluoride for longer time period. In this case whether this methylation status can be used to predict the outcome or severity of the illness supposed to occur ? I hope from your answer this could be used appropriately with an idea of target specific genes.

First of all you have to declare which gene are you looking for? If you know the target gene it is easy to check the methylation status of that gene using specific kit . In that case you should have a control group without long exposure and compare it with the one having long exposure.

Thank you Professor Mahmoudreza Hadjighassem

I am not an expert in this field but my gut feeling is that processes like methylation occur in living cells e.g. plant cell in order to save it from toxic effects due to any environmental factor.If a cell line is treated with a toxin like fluoride ion and then checked for its methylation status, it may indicate whether hyper or hypo methylation occurs.If transcription factors are effected, it will certainly effect the nature of proteins produced , which may be responsible for inhibiting the toxicity factor.

I am not expert in plant cells, you should check with the manufacturer of this kit. but definitely hypermethylation status will change the accessibility of transcription factors, which depend on the site of methylation and how closely it is with Regulatory elements in promoter region.