Trans-kingdom RNA interactions (2)

The roles of structural dynamics in the cellular functions of RNAs 6/10/19

We discuss the mechanisms of gene regulation by microRNAs, riboswitches, ribozymes, post-transcriptional RNA modifications and RNA-binding proteins, and how the cellular environment and processes such as liquid–liquid phase separation may affect RNA folding and activity. The emerging RNA-ensemble–function paradigm is changing our perspective and understanding of RNA regulation, from in vitro to in vivo and from descriptive to predictive.

The creation of RNA is ATP-dependent. The Creation of sunlight and water has been predictably linked from Darwin’s “conditions of life” to all biodiversity on Earth via the physiology of reproduction. See: What is life when it is not protected from virus driven entropy (video)

See for comparison: Multigenerational epigenetic inheritance: One step forward, two generations back 8/27/19

Epigenetic patterns orchestrate gene expression programs that establish the phenotypic diversity of various cellular classes in the central nervous system, play a key role in experience-dependent gene regulation in the adult brain, and are commonly implicated in neurodevelopmental, psychiatric, and neurodegenerative disease states.

These authors claim that research that links trans-kingdom RNA interactions to multigenerational epigenetic inheritance in mammalian species is still in its infancy. See for comparison: From Fertilization to Adult Sexual Behavior (1996). In our Hormones and Behavior review we linked food energy-dependent alternative splicings of pre-mRNAs from the physiology of pheromone-controlled reproduction in yeasts to humans via the conserved molecular mechanisms of microRNA-mediated cell type differentiation.  The term pre-mRNAs was changed to microRNAs, which helps to link our claims to everything known about cell type differentiation in all living genera to protection from the virus-driven degradation of messenger RNA that links mutations to all diseases.

See for comparison: Genomic Enhancers in Brain Health and Disease 1/14/19

Enhancers are non-coding DNA elements that function in cis to regulate transcription from nearby genes. Through direct interactions with gene promoters, enhancers give rise to spatially and temporally precise gene expression profiles in distinct cell or tissue types.

Pseudoscientists use terms like enhancers and promoters because they failed to link the energy-dependent creation of microRNAs from the light-activated assembly of the microRNA-RNA-peptide nanocomplex to biophysically constrained viral latency and the genesis of all biodiversity via the physiology of reproduction in species from microbes to humans.

In Genomic Enhancers in Brain Health and Disease 1/14/19 Energy-dependent gene regulation becomes enhancer-driven gene regulation.


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Regulation of gene expression patterns by genomic enhancers. Illustration of enhancer-promoter chromosomal looping (mediated by CTCF and cohesin) that allows distal enhancer elements to physically interact with and activate gene promoters. These interactions increase binding of transcription factors, chromatin modifiers, and the Mediator complex at gene promoters to recruit RNA polymerase II (RNAPII). Enhancers are characterized by elevated DNA sequence conservation, open chromatin, transcription factor binding motifs, characteristic histone modifications, DNA hypomethylation, and bidirectional transcription to generate enhancer RNAs (eRNAs).

The light-activated assembly of the microRNA-RNA-peptide nanocomplex becomes the mediator complex, which automagically links bidirectional transcription to the generation of enhancer RNAs (eRNAs).

In the world of biologically uninformed science idiots who fail to link the Creation of anti-entropic virucidal light and the Creation of water to the hydrophobicity of supercoiled DNA, pseudoscientists need only start with the generation of enhancer RNAs, to avoid the complexity of the ATP-dependent creation of RNA, which has linked the physiology of reproduction to the biogenesis of all diversity on Earth since 1964.

See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

See also: UPFront and center in RNA decay: UPF1 in nonsense-mediated mRNA decay and beyond 1/17/19

Nonsense-mediated mRNA decay (NMD), which is arguably the best-characterized translation-dependent regulatory pathway in mammals, selectively degrades mRNAs as a means of post-transcriptional gene control. Control can be for the purpose of ensuring the quality of gene expression. Alternatively, control can facilitate the adaptation of cells to changes in their environment. Key to NMD, no matter what its purpose, is the ATP-dependent RNA helicase upstream frameshift 1 (UPF1), without which NMD fails to occur. However, UPF1 does much more than regulate NMD. As examples, UPF1 is engaged in functionally diverse mRNA decay pathways mediated by a variety of RNA-binding proteins that include staufen, stem-loop-binding protein, glucocorticoid receptor, and regnase 1. Moreover, UPF1 promotes tudor-staphylococcal/micrococcal-like nuclease-mediated microRNA decay. In this review, we first focus on how the NMD machinery recognizes an NMD target and triggers mRNA degradation. Next, we compare and contrast the mechanisms by which UPF1 functions in the decay of other mRNAs and also in microRNA decay. UPF1, as a protein polymath, engenders cells with the ability to shape their transcriptome in response to diverse biological and physiological needs.

Simply put, energy-dependent changes in the microRNA/messenger RNA balance must be linked to all biophysically constrained biodiversity via the physiology of reproduction, which biophysically constrains food energy-dependent pheromone-controlled trans-kingdom RNA interactions. For comparison, claims about enhancer-driven multigenerational epigenetic inheritance are ridiculous.




Author: James Kohl

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