From 3-D to epigenetically-effected 4-D genome make-up

By: James V. Kohl | Published on: February 25, 2015

Discoveries in 3-D Genome Make-Up and Genetic Changes: Clarification of differences amidst chromosome pairs and how gene expression is effected by chromosome folding

Excerpt: “…offers a useful guide for future studies of the epigenome’s function in our evolution and diseases that beset us.”
My comment: The guide is also useful because it shows how the anti-entropic effects of light-induced amino acid substitutions links the epigenetic landscape to the physical landscape of DNA in species from microbes to man. For example, light is epigenetically trapped by water molecules and linked from its spectral energy to food energy.
Food energy is epigenetically trapped by the de novo creation of receptors that enable nutrients to enter cells. The cells that acquire the nutrients differentially adapt to ecological variation in their energy source.
The adaptations are manifested in their nutrient-dependent physiology of reproduction. The physiology of reproduction links fixation of the amino acids substitutions to the differentiation of all cell types in all individuals of all ecologically adapted species.
The links from entropic elasticity to 3-D genome make-up have already been placed into the context that clarifies how differences in chromosomal rearrangements and gene expression arise in the context of RNA-directed DNA methylation and RNA mediated amino acid substitutions that alter chromatin loops and protein folding during life history transitions of species from microbes to man. The life history transitions are addressed in the context of 4-D genome make-up, which has not been addressed in the context of evolution.
Evolutionary theorist have only recently begun to realize that mutations linked to perturbed protein folding cannot also be linked via evolution to increasing organismal complexity — except in ridiculous theories based on the definition of “mutation” and assumptions about how long it would take accumulated mutations to lead from one species to a new species. The obvious answer to that question is: NEVER!
See Inching toward the 3D genome for more information and my comments on how understanding life history transitions is being explored in the context of the 4D genome.
My comment to the Science site:
Re: “…the nucleome structure changes as cells age, differentiate, and divide, and researchers want to understand how and why.”
Cell type differentiation is nutrient-dependent. RNA-directed DNA methylation links RNA-mediated amino acid substitutions to cell type differentiation via protein folding during life history transitions. Amino acid substitutions stabilize protein folding; mutations perturb it, during nutrient-dependent theromodynamic cycles of protein biosynthesis and degradation.
Life is physics and chemistry and communication
The metabolism of nutrients links metabolic networks to genetic networks via species-specific pheromones that control the physiology of reproduction. Simply put, pheromones link nutrient-dependent life via physics, chemistry, and the conserved molecular mechanisms of communication in species from microbes to man.
Nutrient-dependent protein folding is linked via the conserved molecular mechanisms of amino acid substitutions and pheromone-controlled DNA stability in organized genomes. The stability links the epigenetic landscape to the physical landscape of DNA. That means researchers who do not understand biologically-based cause and effect must take a piece-meal approach to integrating the requirements for life and successful life history transitions — despite the fact that life history transitions have been detailed in the context of the honeybee model organism. See: Honey bees as a model for understanding mechanisms of life history transitions
In January 2015, researchers reported links from all crustaceans to all insects that made the differences in species appear to be difference in species of Biblical “like kind.”See: All of “like kind” in the (bigger) family
Nothing suggests that the most divergent organisms on the Earth somehow evolved their biodiversity.  Everything currently know about how atoms and ecosystems are epigenetically linked attests to the fact that light-induced amino acid substitutions stabilize the organized genome. Amino acid substitutions enable the entropic elasticity of epigenesis and epistasis that is prevented by viral microRNAs. Nutrient-dependent microRNAs also alter the microRNA/messenger RNA balance and prevent the viral microRNAs from perturbing the biosynthesis and/or degradation of proteins. See: All of “like kind” (Part 2)

Discoveries in 3-D Genome Make-Up and Genetic Changes: Clarification of differences amidst chromosome pairs and how gene expression is effected by chromosome folding

Excerpt 2)
“The paper titled “Integrative Analysis of Haplotype-Resolved Epigenomes Across Human Tissues,” is found here:
The paper titled “Chromatin Architecture Reorganization during Stem Cell Differentiation,” is found here:
My comment: Epigenomics: Roadmap for regulation
Excerpt: “A case in point is modification of the amino-acid residue lysine 27 (K27) on histone H3 in chromatin. Addition of an acetyl group (a modification known as H3K27ac) correlates with transcription of the corresponding region of DNA, whereas trimethylation (H3K27me3) is linked to transcriptional repression.”
See also: Long noncoding RNA-directed epigenetic regulation of gene expression is associated with anxiety-like behavior in mice reported as Hidden gene gives hope for improving brain function
Excerpt: “The gene is a long, noncoding RNA and was found within a section of the genome most commonly associated with “junk” DNA – the 98 per cent of the human genome that, until recently, was thought to have no function. This is the first time long, noncoding RNA activity has been detected in the brain in response to experience.”
My comment: The gene (DNA) is RNA and RNA activity “…has been detected in the brain in response to experience.” Yet, supposedly, “This is the first time… RNA activity has been detected in the brain in response to experience.” The journalist appears to have missed the most obvious correlation with what is now being discussed in the context of top-down causation and 4-D genome make-up that changes during life history transitions. See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults. It shows the difference that a single nutrient-dependent RNA-mediated amino acid substitution can make during experience-dependent life history transitions that link metabolic networks to genetic networks in species from microbes to humans via the conserved molecular mechanisms of biophysically constrained protein folding that links physics to chemistry and information transfer to biology.
See also: N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions reported as Epigenetic ‘switch’ regulates RNA-protein interactions
Excerpt: Article summary: “Epigenetic modifications to mRNA act as a structural ‘switch’ that allows RNA-binding proteins to recognize and read mRNA regions that would otherwise be inaccessible, a new study has found. The findings provide a new understanding of this emerging field of study.”
My comment: See our section on molecular epigenetics, for comparison: From Fertilization to Adult Sexual Behavior  Also see my unpublished invited review: “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.”

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