Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA
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Reported as
Scientists discover RNA modifications in some unexpected places
Excerpt 1): “…there are multiple types of RNA, three of which—messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)—are essential for proper protein production. Moreover, RNAs that are synthesized during the process known as transcription often undergo subsequent changes, which are referred to as “post-transcriptional modifications.”
My comment: These microRNA/messenger RNA-mediated events (above) are essential for proper protein production (PPP). The epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man via RNA-mediated PPP.
‘Genome Dynamics Events’ is another term for ‘RNA-mediated.’ No matter which term is used, RNA-mediated amino acid substitutions lead to cell type differentiation via nutrient-dependent PPP in species from microbes to man. For example, nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation lead to amino acid substitutions that are fixed in the organized genomes of all species via epigenetic effects of the nutrient-dependent pheromone-controlled physiology of reproduction. Fixation occurs only if the amino acid substitutions thermodynamically stabilize the organized genome and lead to PPP, which is manifested in organism-level thermoregulation.
Nutrient stress and social stress thermodynamically perturb PPP. Perturbed thermodynamic cycles of protein biosynthesis and degradation (i.e., PPP) are associated with nutrient stress and social stress via associations with the epigenetic effects of food odors and pheromones on the de novo Creation of odor receptor genes. The experience dependent de novo Creation of odor receptor genes links extreme forms of nutrient stress, like starvation, and social stress, like trauma, to perturbed PPP. Pertubed PPP results in mutations, which are not beneficial. Cell type differentiation cannot occur normally in the context of perturbed PPP.
Excerpt 2:) “…these findings suggest that heat shock activates a dynamic pseudouridylation program in yeast that may lead to beneficial outcomes for the organism, perhaps by increasing mRNA stability under adverse conditions.”
My comment: Heat shock proteins (HSPs) respond to the challenges of ecological variation in organisms ranging from bacteria to humans. Transcription of HSPs is primarily regulated by transcription factors, one of which plays a dominant role in stress responses, while others function in normal cellular processes. In the context of organism level thermoregulation, the HSPs link nutrient stress and social stress to RNA-mediated events that differentiate cell types via amino acid substitutions. Cell type differentiation does not occur in the context of severe nutrient stress, like starvation, because no amino acids can be produced. Cell type differentiation via amino acid substitutions and PPP may not occur in the context of severe social stress because feedback mechanisms of intercellular signaling lead to the same changes in cells that are starving to death.
The remarkable similarities in RNA-mediated events that epigenetically effect cell type differentiation via amino acid substitutions in yeasts and humans were detailed in the molecular epigenetics section of our 1996 Hormones and Behavior review. However, researchers have been more interested in how RNA-mediated events may be involved in a number of human diseases associated with mutations in different genes. They have largely missed the significance of RNA-mediated events we detailed in the context of sex differences in cell type. Now these researchers seem to be most interested in RNA-mediated events linked to pseudouridylation in human pathologies. I remain interested in how all RNA-mediated events associated with nutrient stress and social stress are linked to typical healthy cell type differentiation and atypical cell type differentiation, which is linked to all diseases and disorders via conserved molecular mechanisms.
