A two-faced protein enables RNA-mediated DNA repair (2)

By: James V. Kohl | Published on: December 8, 2015

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A two-faced protein enables RNA-mediated DNA repair
See also: Abundant contribution of short tandem repeats to gene expression variation in humans (subscription required)
Excerpt:

…suggesting that STRs have a key role in the evolution of expression. Indeed, several candidate gene studies in humans reported that STR variations modulate gene expression19,33–37 and alternative splicing…

Reported as:

Researchers find repetitive DNA provides a hidden layer of functional information

Excerpt:

He is calling these variants eSTRs, or expression STRs, to note that they regulate gene expression.

My comment: He is not calling the variants mutations, which means he is not linking mutations to evolution. Instead, he is one step away from calling them microRNAs. A recent PubMed search using the term “microRNA” revealed more than 45,000 published reports. Most of them were published in just the past few years.
Apparently, many serious scientists have been using terms like pre-mRNAs, small RNAs, non-coding RNAs, microRNAs, and QTLs. Some serious scientists have defined the terms they are using to link nutrient energy-dependent RNA-mediated cause and effect to cell type differentiation in all living genera. Some have not. In the mid-1990s, we linked them From Fertilization to Adult Sexual Behavior in species from microbes to humans via the physiology of reproduction without defining the term pre-mRNA. Instead, we used the term in its proper context.
The fact that Yaniv Erlich uses eSTRS rather that pre-mRNAs or other terms is irrelevant. He may confuse others with yet another change of the term. But no matter what you call the variants, they link atoms to ecosystems via nutrient energy-dependent base pair changes and RNA-mediated events, which link the physiology of reproduction to RNA-mediated amino acid substitutions and cell type differentiation in all cells of all individuals of all living genera.
For example, Yaniv Erlich co-authored this journal article.
See also: Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs
Abstract excerpt:

Synthetic microRNA (miRNA) mimetics, viral miRNAs expressed by infected B cells, and endogenous miRNAs could all be transferred into T cells. These mechanisms may allow small RNA-mediated communication between immune cells.

Conclusion:

Given the propensity of viruses to exploit such opportunities, it seems likely that the studies presented herein will prompt more investigation of the nonautonomous effects of small RNAs in contexts where an advantage may be gained by immune modulation. Moreover, our results also raise the possibility that transfer of small RNAs will be a general principle encountered when other cell types establish the types of contacts represented by example in immune cells.

See our section on: Immunological Factors
Excerpt:

The immune system has long been known to perceive certain sexual differences, e.g., the presence or absence of H-Y antigen (Simpson, 1991). Mice have been shown to enact kin selection on the basis of major histocompatibility complex characteristics within the perceiving mice and from other mice as chemosensitive identified. Humans have been shown to possess similar immune- related chemosensitive skills (Gilbert, Yamazaki, Beauchamp, and Thomas, 1996; Wedekind, Seebeck, Bettens, and Paepke, 1995).

My comment: The fact that the innate immune system links the epigenetic landscape to the physical landscape of DNA via RNA-mediated cell type differentiation has been obvious to most serious scientists for at least two to four decades. The fact that the innate immune system is nutrient-dependent, which links it from cell type differentiation to the physiology of reproduction via food odors and pheromones has been obvious for at least one decade. See: Feedback loops link odor and pheromone signaling with reproduction
See for comparison: Convergent evolution of neural systems in ctenophores
Excerpt:

…comb jellies are carnivorous marine animals with a complex neuromuscular organization and sophisticated patterns of behavior. To sustain these functions, they have evolved a number of unique molecular innovations supporting the hypothesis of massive homoplasies in the organization of integrative and locomotory systems.

Conclusion:

Together with numerous ctenophore ‘innovations’, ctenophores may serve as a model to understand the origins or emergence of complex integrative functions and can be used in synthetic biology and regenerative medicine to design novel regulatory systems.

My comment: The sequencing of the octopus genome has since linked the conserved molecular mechanisms of RNA-mediated cell type differentiation from microbes to man via what has been learned about microRNAs and cell adhesion proteins in the context of supercoiled DNA that protects all organized genomes from virus-driven entropy.
See: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity
And: The octopus genome and the evolution of cephalopod neural and morphological novelties
Excerpt:

Taken together, these novel genes, the expansion of C2H2 ZNFs, genome rearrangements, and extensive transposable element activity yield a new landscape for both trans- and cis-regulatory elements in the octopus genome, resulting in changes in an otherwise ‘typical’ lophotrochozoan gene complement that contributed to the evolution of cephalopod neural complexity and morphological innovations.

And see: A Protocadherin-Cadherin-FLRT3 Complex Controls Cell Adhesion and Morphogenesis
My comment: It seems clear that nutrient-dependent microRNAs and cell adhesion proteins protect the organized genomes of all living genera from virus-driven entropy. However, there still seem to be questions about how to place that fact into the context of evolution via natural selection of anything except food or via mutations that are linked to loss of function via virus-perturbed protein folding chemistry. This poses some conflict among those who teach neuroscience outside the context of religion, and only one professor seems to be teaching both in the same course.
See:
https://www.dailymotion.com/video/x2qkadf