Positive feedback loops and epigenetic traps

By: James V. Kohl | Published on: November 23, 2015

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Transcription factor trapping by RNA in gene regulatory elements

Conclusion:

…bidirectional transcription of active enhancers and promoters evolved, in part, to facilitate trapping of TFs at specific regulatory elements. The model also suggests that transcription of regulatory elements produces a positive-feedback loop that may contribute to the stability of gene expression programs in cells. The contribution of this TF trapping mechanism to cellular regulation has yet to be established but will be important to elucidate in future studies because much disease-associated sequence variation occurs in enhancers (20, 22) and may thus affect both DNA and RNA sequences that interact with gene regulators.

My comment: Bidirectional transcription did not evolve. It is nutrient-dependent and controlled by the physiology of reproduction. Feedback loops link odor and pheromone signaling with reproduction in species from microbes to humans. That fact links RNA-mediated gene duplication and RNA-mediated amino acid substitutions to the stability of organized genomes via what is known about supercoiled DNA. Supercoiled DNA protects the organized genomes of all living genera from virus-driven entropy.
Researchers who consistently fail to recognize the fact that supercoiled DNA is an epigenetic trap also seem reluctant to acknowledge the epigenetic trap that Schrodinger claimed linked the anti-entropic effect of the sun’s biological energy life on Earth in What is Life?
Excerpt:

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

My comment: By ignoring the epigenetic trap that links sunlight on contact with water to the energy spectrum manifested in the range from ultraviolet to infrared light, researchers become like theorists who must link the nutrient-dependent biophysically constrained chemistry of RNA-mediated protein folding in their ridiculous claims about mutations and evolution. For example: “…bidirectional transcription of active enhancers and promoters evolved…”
Stop the nonsense! Force all researchers to report their findings in terms of how ecological variation is linked to ecological adaptations via what is currently known about the stability of nutrient-dependent genome organization in all living genera.
See also: Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast and Stable recombination hotspots in birds
reported as: Putting the breaks on meiosis and predicted in Combating Evolution to Fight Disease
Conclusion:

“…an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.”

My comment: The genesis of variation is nutrient-dependent and nothing evolves from anything else. All living genera exemplify links between ecological variation and ecological speciation that is nutrient-dependent and controlled by the physiology of reproduction.
See also: Long non-coding RNAs as a source of new peptides, but stop claiming that there is any such thing as de novo protein evolution. Claims that proteins or species evolve are made only by the biologically uninformed.