Epigenetic Study - (Nov/10/2008 )

Hello everyone,

Has anyone looked at epigenetic states in human disease? I am trying to determine epigenetic changes in a human model. I am proposing to remove adipose tissue and then do a ChIP-chip assay on the DNA. I am a biochemist trying to understand epigenetic methodology.

Does anyone know how to fix the state of DNA methylation/histone modification? I am worried about changes from the extraction to the methylation states without fixing it.

Your response is appreciated.

Thanks,

-uawildcat2008-

ChIP assay on tissue samples is possible and there are protocols for crosslinking protein and DNA in tissue sample. Once crosslink is done, DNA bound proteins such as histones, methylated CpG binding proteins etc remain bound to DNA so that you will be able to get a snap picture of epigenetic status of the DNA.

-pcrman-

In your opinion is Chip-Chip assay the best for studying epigenetic alterations genome-wide?

Also, I have read many people's articles on different types of histone modifications. It seems that H3K9, and H3K4 acetylation and methylation are the most recognized and understood. Is this a good place to start for epigenetic histone modifications?

Thanks,

-uawildcat2008-

depends what are you looking for, are you looking for gene activation or gene suppression. Different histone modifications have different function. I personally think acetylation of histone is usually very dynamic and only temporary changes where as methylation is more inheritance.

of course it is good to start from those sites u were mentioning. But also try to look at H3K27 Methylation. =)

-timjim-

my two cents would be to also incorporate genome-wide expression data to your study as that is a good endpoint to look at in your system.

Nick

-methylnick-

my two cents would be to also incorporate genome-wide expression data to your study as that is a good endpoint to look at in your system.

Nick

-methylnick-

Hello again,

I have come to find out that there are numerous histone residues that can be either modified. Is there an expert who can say which ones would be the most interesting to study... I am definitely going to study DNA methylation, and probably up to 10-20 histone modifications.

Please advise.

Thanks,

-uawildcat2008-