De novo DNA methylation?

By: James V. Kohl | Published on: October 31, 2014

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Epigenomics and the control of fate, form and function in social insects

Excerpt: “De novo DNA methylation is critical for developmental divergence of female larvae towards the honeybee worker caste and is progressive [49,51].”

de novo is a Latin expression meaning “from the beginning

DNA methylation does not automagically occur. From the beginning, it has been nutrient-dependent and RNA-directed. Nutrient-dependent RNA-directed DNA methylation links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. If de novo DNA methylation automagically occurred, there would be no link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.
In the honeybee model organism and other model organisms, RNA-directed DNA methylation links nutrient-dependent amino acid substitutions to cell type differentiation in all cells via conserved molecular mechanisms. The metabolism of nutrients to pheromones controls the differentiation of cell types that result in the morphological and behavioral phenotypes of every bee in the hive.
The article that suggests de novo DNA methylation automagically occurs appears to place nutrient-dependent RNA-directed DNA methylation and RNA-mediated cell type differentiation by amino acid substitutions into the context of the evolution of biodiversity. First, the authors link the automagical evolution of biodiversity manifested in the morphological and behavioral phenotypes of species from microbes to man to de novo methylation. Then, the authors add “… nutrition may have a significant and direct role in directing patterns of epigenomic control during developmental caste determination.’
See for comparison: Nutrition and epigenetics: an interplay of dietary methyl donors, one-carbon metabolism and DNA methylation
“Epigenetic modifications include chromatin remodeling, histone tail modifications, DNA methylation and, more recently, have expanded to include non-coding RNA and microRNA gene regulation [3].
DNA methylation is the most widely studied form of epigenetic modification and occurs within the one-carbon metabolism pathway, which is dependent upon several enzymes in the presence of dietary micronutrients as cofactors, including the availability of folate, choline and betaine through the diet (Fig. 1). Through an ATP-driven reaction, methionine is converted into S-adenosylmethionine (SAM), the universal cellular methyl donor [4]. DNA methyltransferases (DNMTs) covalently attach methyl groups from SAM to the carbon-5 position of cytosine bases, generating 5-methylcytosine thus methylating DNA.”
Here are some differences between de novo DNA methylation and nutrient-dependent DNA methylation in the context of the evolution of biodiversity.
1) There is no such thing as de novo DNA methylation. That means there is no such thing as de novo RNA-mediated cell type differentiation by amino acid substitutions, which differentiate the cell types of all individuals of all species.
2) Nutrient-dependent RNA-directed DNA methylation links RNA-mediated cell type differentiation by amino acid substitutions to the differentiation of cell types in all individuals of all species.
Summary, cell type differentiation that occurs via nutrient-dependent amino acid substitutions is controlled by the metabolism of nutrients to species-specific pheromones. The pheromones control the physiology of nutrient-dependent reproduction, which links it from RNA-directed DNA methylation to pheromone-controlled fixation of the amino acid substitutions that differentiate all cell types via conserved molecular mechanisms in species from microbes to man.
For examples, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Also see, Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB for the most recent publication on nutrient-dependent amino acid substitutions that differentiate the cell types of bacteria in the context of antibiotic resistance previously reported to be driven by mutations that somehow caused bacteria and other species to evolve.

See also: Jack A, Connelly J. J, Morris J. P. DNA methylation of the oxytocin receptor gene predicts neural response to ambiguous social stimuli. Frontiers in Human Neuroscience. 2012;6:280.
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