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Isolating a gene or sets of genes in diseases sometimes isn't enough to determine penetrance - epigenetic factors can have a significant effect. What are the criteria in determining whether epigenetic factors are significant?

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First of all, the nature of penetrance is almost entirely unknown. Likely it's a combination of epistasis and gene interactions, induced gene regulatory pathways, developmental noise, and other factors. Epigenetics (imprinting, etc) may have little to do with penetrance, while chromatin structure may be a consequence of other things (most now regard histone modifications, etc, as consequence of transcription rather than heritable regulatory mechanism). Currently, the field of epigenetics is undergoing a (long-overdue) reassessment. Until that happens, anyone who wants to make claims of "epigenetics" is free to, so spurious claims are rampant.

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Do you know any relevant papers/reviews on the issue? –  nico Dec 26 '11 at 15:57
    
Sorry, reviews on which? Penetrance, epigenetics, or chromatin structure? –  KAM Dec 29 '11 at 21:32
    
Sorry, my comment was not clear. I was wondering if there were reviews on the current view of epigenetics. You are saying that the field needs a reassessment, I was wondering if someone had analysed this issue in detail (why it need it, what are the things to better define etc) –  nico Dec 29 '11 at 23:27
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A few years ago Youngson and Whitelaw wrote a review that started to separate epigenetics from inducible gene expression (chd.ucsd.edu/_files/winter2009/…), but it didn't go far enough. There have been studies lately that show that histone modifications are probably consequence of gene expression, rather than carrying memory. Similarly there are studies that show that DNA methylation does not "shut off" expression, and there is still not a single case showing that methylation changes alter endogenous gene expression. –  KAM Dec 30 '11 at 11:19
    
Thanks, that is a good start. So, correct me if I am wrong, you are saying that it has been been shown that the methylation status can change depending on gene transcription, but not that methylation modulates transcription? –  nico Dec 30 '11 at 11:33
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