Summary: Energy determines genome compaction because activity in the nucleus is energy-dependent. Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction. It’s all about the base.
The chromatin structure of DNA determines genome compaction and activity in the nucleus.
My comment: Energy determines genome compaction because activity in the nucleus is energy-dependent.
Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.
My comment: Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction.
Besides potentially upending the textbook model of DNA organization, the team’s results suggest that controlling access to chromatin could be a useful approach to preventing, diagnosing and treating diseases such as cancer.
“We show that chromatin does not need to form discrete higher-order structures to fit in the nucleus,” adds O’Shea. “It’s the packing density that could change and limit the accessibility of chromatin, providing a local and global structural basis through which different combinations of DNA sequences, nucleosome variations and modifications could be integrated in the nucleus to exquisitely fine-tune the functional activity and accessibility of our genomes.”
The packing density of supercoiled DNA is energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera. Sunlight is the source of all biophysically constrained energy on Earth.The anti-entropic virucidal effect of sunlight biophysically constrains the degradation of messenger RNA.
Virus-driven energy theft causes negative supercoiling of supercoiled DNA. Without food energy-dependent RNA-mediated DNA repair (autophagy), viruses cause the degradation of messenger RNA that links mutations to all pathology. The sun’s anti-entropic virucidal energy links changes in chirality to autophagy and the de novo creation of enzymes, hormones and receptors that are needed to protect all organized genomes from viruses.
The textbook model of DNA organization was represented in Mutation-driven evolution for comparison to “Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day more than 4 years ago.
Masatoshi Nei used an ambiguous definition of mutation and linked any energy-dependent nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc, (any change in the structure of supercoiled DNA) from natural selection to an evolutionary process initiated by mutation.
In my review, I used examples of food energy-dependent changes in base pairs to link the honeybee model of nutrient-dependent pheromone-controlled biodiversity to a history of published works that began with The Scent of Eros: Mysteries of Odor in Human Sexuality (reviewed by Mark Sergeant)
The index from The Scent of Eros: Mysteries of Odor in Human Sexuality may help others to establish all the known links from the energy-dependent de novo creation of microRNAs to the creation of G protein-coupled receptors and gonadotropin releasing hormone (GnRH) secretion, which was linked to all biodiversity. See, for example, these entries from page 217:
See also: Cytosis: A Cell Biology Board Game
A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
See also: Energy-dependent physical and biophysical constraints (10) in prep