Uniquely epigenomic gene regulation

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development


Methylation at alternative promoters or splice sites can affect transcript variants expression, whereas enhancer methylation may modulate gene expression (Jones, 2012). These are potential mechanisms for translating DNA methylation information to phenotypes.

Reported as:

Reprogramming of DNA observed in human germ cells for first time


…a notable fraction of the retroelements in our genome are ‘escapees’ and retain their methylation patterns – particularly those retroelements that have entered our genome in our more recent evolutionary history. This suggests that our body’s defence mechanism may be keeping some epigenetic information intact to protect us from potentially detrimental effects.

My comment: The conserved molecular mechanisms of cell type differentiation are RNA-directed and they link DNA methylation to RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all genera. The anti-entropic epigenetic effects of nutrient-dependent microRNAs prevents the entropic elasticity attributed to viral microRNAs from leading to genomic entropy.
The balance of nutrient-dependent microRNAs and viral microRNAs alters the thermodynamic cycles of protein biosynthesis and degradation. These cycles link fixation of amino acid substitutions to cell type differentiation. The thermodynamic cycles also link viruses and viral microRNAs to perturbed protein folding and pathology. Healthy cell type differentiation can be viewed in the context of how it occurs in species from yeasts to primates.
See: From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation….

See: Feedback loops link odor and pheromone signaling with reproduction; Signaling Crosstalk: Integrating Nutrient Availability and Sex
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Cell type differentiation is typically biophysically constrained by the nutrient-dependent chemistry of RNA-mediated protein folding, which links RNA-mediated amino acid substitutions to morphological phenotypes and behavioral phenotypes via metabolic networks linked to genetic networks.
Past protection from the damage caused by viruses and viral microRNAs, which would otherwise be linked to genomic entropy, continues in the context of the physiology of nutrient-dependent reproduction.  Transgenerational epigenetic inheritance of organized genomes helps to ensure that what promoted survival in the past continues to promote it in future — until some day the viruses kill us all. Until then, claims like this one should be viewed with suspicion by serious scientists:
Excerpt from Mutation-Driven Evolution (p. 199):

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.

That suspicious claim can be compared to what was reported as “re-evolution” of the bacterial flagellum in 4 days. One mutation was not enough. Two were required and both were linked to amino acid substitutions. If the researchers had learned the difference between mutations that perturb protein folding and amino acid substitutions that stabilize it, they might have accurately reported that ecological variation led to ecological adaptation via the nutrient-dependent pheromone-controlled creation of the missing flagellum. Instead, see:

Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.


Bacteria that lack a vital protein for growing flagella—tail-like structures that enable the microbes to swim—can attain flagella in as little as four days given enough pressure to evolve, according to a paper published in Science today (February 26).


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