Epigenetic switch links MicroRNAs to RNA-protein interactions
N6-methyladenosine marks primary microRNAs for processing
Excerpt: “Our findings reveal that the m6A mark acts as a key post-transcriptional modification that promotes the initiation of miRNA biogenesis.”
Excerpt: “… these experiments have identified a switch that can be used to ramp up or tamp down microRNA levels, and as a result, alter gene expression”
My comment: The ‘m6A-switch’ aka the ‘m6A mark’ appears to link ecological variation to nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all genera via the biophysically constrained chemistry of RNA-mediated protein folding.
See also: N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions
Excerpt: “…these results confirmed that m6A modification can alter its local RNA structure and enhance the accessibility of its base-paired residues or nearby regions to modulate protein binding (Fig. 1f).”
Excerpt: “RNA epigenetic modifications affect practically all RNA-protein interactions,” said senior study author Tao Pan, PhD, professor of biochemistry and molecular biology at the University of Chicago. “This ‘switch’ mechanism is expected to work as a master regulator of wide-ranging biological activities through influencing RNA-protein interactions.”
My comment: Ecological variation and the metabolism of nutrients to species-specific pheromones controls the physiology of reproduction in species from microbes to man. Ecological variation links the viral microRNA/nutrient-dependent microRNA balance to pheromone-controlled fixation of amino acid substitutions at the origins of plant life in the context of light-induced amino acid substitutions in plants and algae and sea-slugs et al. Search Results for ‘sea slug’
Dobzhansky (1973) provided an example of an amino acid substitution linked to biodiversity in species of Biblical “like kind.”
Excerpt: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla” (p. 127).
The link from microRNA’s to cell type differentiation in species of Biblical “like kind” also was reported in All in the (bigger) family
Excerpt: Jerome Hui of the Chinese University of Hong Kong found that in both insects and crustaceans, the same set of micro RNAs control expression of the genes for those enzymes.
See also: The phylogenetic utility and functional constraint of microRNA flanking sequences
Excerpt: “Our investigation demonstrates the utility of miRNA sequences as classical phylogenetic markers, and shows this usage is robust to different algorithms of phylogenetic analysis and the analysis of fast-evolving lineages.”
My comment: The fast evolving lineages must be placed into the context of how ecological variation leads to nutrient-dependent pheromone-controlled ecological adaptations in organisms of Biblical “like kind” via RNA-mediated amino acid substitutions whether they are in primates or insects or crustaceans. There is no experimental evidence that suggests the conserved molecular mechanisms of cell type differentiation vary in species from microbes to man. See the molecular epigenetics section of our 1996 Hormones and Behavior review for examples of RNA-mediated cell type differentiation and the mechanisms that enable it. From Fertilization to Adult Sexual Behavior
See also my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract: “This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.”
The invited review was returned “without review” because no one would review it. I’m not sure whether the problem was the complexity of systems biology or if the problem was the likelihood that the potential reviewers were theorists who never learned how to link physics, chemistry, and information via molecular biology to biodiversity. Indeed, some of them may believe “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world” (p. 199).
That’s probably what most of them were taught to believe in, and not to question. The obvious problem is that “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.” — Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble
Once people are taught to believe in pseudoscientific nonsense, it’s harder to interest them in learning about the biological basis of nutrient-dependent cause and effect. See also: Luis P. Villarreal: We Need a Nonlinear Language for Life Excerpt: There are actually relatively few formally-trained evolutionary scientists who will accept the virus-first perspective.
See also: Force for ancient and recent life: viral and stem-loop RNA consortia promote life
Excerpt: “…the massive creative power of a cooperative RNA consortium (QS-C) remains crucial for life. QS-C was made known to us only recently by virus evolution (e.g., HIV-1). Its role in the origin of life, the emergence of complexity and the creation of group identity should now receive our combined attention.”
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