Mark Ptashne, Oliver Hobert, and Eric Davidson talk sense on epigenomics:

We were astonished to see two sentences in your Editorial on the International Human Epigenome Consortium (Nature 463, 587; 2010) that seem to disregard principles of gene regulation and of evolutionary and developmental biology that have been established during the past 50 years.

You say: “By 2004, large-scale genome projects were already indicating that genome sequences, within and across species, were too similar to be able to explain the diversity of life. It was instead clear that epigenetics — those changes to gene expression caused by chemical modification of DNA and its associated proteins — could explain much about how these similar genetic codes are expressed uniquely in different cells, in different environmental conditions and at different times.”

With respect to 'epigenomics', we wish to stress that chromatin 'marks' and local chemical modifications of DNA, such as methylation, are the consequences of DNA-sequence-specific interactions of proteins (and RNA) that recruit modifying enzymes to specific targets. They are thus directly dependent on the genomic sequence. Such marks are the effects of sequence-specific regulatory interactions, not the causes of cell-type-specific gene expression.

The idea that genomes between species are too similar to account for species diversity is absolute nonsense. And so is the idea that epigenetic information is completely independent of DNA sequence.

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