De novo DNA methylation?

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.

Also see:

Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses.

About James V. Kohl 1308 Articles
James Vaughn Kohl was the first to accurately conceptualize human pheromones, and began presenting his findings to the scientific community in 1992. He continues to present to, and publish for, diverse scientific and lay audiences, while constantly monitoring the scientific presses for new information that is relevant to the development of his initial and ongoing conceptualization of human pheromones. Recently, Kohl integrated scientific evidence that pinpoints the evolved neurophysiological mechanism that links olfactory/pheromonal input to genes in hormone-secreting cells of tissue in a specific area of the brain that is primarily involved in the sensory integration of olfactory and visual input, and in the development of human sexual preferences. His award-winning 2007 article/book chapter on multisensory integration: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences followed an award winning 2001 publication: Human pheromones: integrating neuroendocrinology and ethology, which was coauthored by disinguished researchers from Vienna. Rarely do researchers win awards in multiple disciplines, but Kohl’s 2001 award was for neuroscience, and his 2007 “Reiss Theory” award was for social science. Kohl has worked as a medical laboratory scientist since 1974, and he has devoted more than twenty-five years to researching the relationship between the sense of smell and the development of human sexual preferences. Unlike many researchers who work with non-human subjects, medical laboratory scientists use the latest technology from many scientific disciplines to perform a variety of specialized diagnostic medical testing on people. James V. Kohl is certified with: * American Society for Clinical Pathology * American Medical Technologists James V. Kohl is a member of: * Society for Neuroscience * Society for Behavioral Neuroendocrinology * Association for Chemoreception Sciences * Society for the Scientific Study of Sexuality * International Society for Human Ethology * American Society for Clinical Laboratory Science * Mensa, the international high IQ society