RNA-directed

Retinoic acid + one receptor regulate the genome

See also: Epigenetics: microRNAs effect an integrative pathway for my additional comments on Master orchestrator of the genome is discovered, stem cell scientists report) Retinoic acid is a metabolite of vitamin A (retinol) that mediates the functions of vitamin A required for growth and development. The fibroblast growth factor receptor 1 “…gene provides instructions for making a protein called fibroblast growth factor receptor 1. This protein is one of four fibroblast growth factor receptors, which are related proteins that are…

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Epigenetics: microRNAs effect an integrative pathway

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1) Excerpt 1) The accumulation of hypoglycosylated nuclear FGFR1 (nFGFR1) is stimulated by a variety of developmental signals, including various growth factors, hormones, and neurotransmitters as well as a reduction in cell contact. This is the reason that this pathway is referred to as integrative [1, 15]. Reported as: Master orchestrator of the genome is discovered, stem cell scientists report Summary: New research shows how a single…

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Tissue type variation and expression of genes

Exploring the Impacts of Genetic Variation on Tissue-Specific Expression Preliminary results from the Genotype-Tissue Expression project reveal that gene expression varies more across tissues than across individuals. By Jenny Rood | May 7, 2015 Excerpt: “You’ve got the genetic variation, you’ve got the gene expression levels, you’ve got the different tissues…” My comment: What you don’t have is a model of RNA-directed DNA methylation and RNA-mediated amino acid substitutions that links the epigenetic landscape to the physical landscape of DNA…

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Chance mutations — not natural selection

A Surprise for Evolution in Giant Tree of Life Excerpt (with my emphasis): Each variant adapted to suit a different ecological niche. But Blair Hedges, a biologist at Temple University in Philadelphia, has proposed a provocative alternative: Adaptation had little to do with it. It was simply a matter of chance and time. See also: The Surprising Origins of Evolutionary Complexity July 16, 2013 Excerpt: Some argue that life has a built-in tendency to become more complex over time. Others…

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Viruses in gut microbes

Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells 5/4/15 Excerpt: Extended Data Figure 3 | Generation of H3.3-isoform-specific antibodies. Related to Fig. 1. a, Schematic of amino acid sequence differences for the canonical histones H3.1 and H3.2 versus the histone variant H3.3. H3.3 differs from H3.2 or H3.1 at only 4 or 5 amino acids, positions 31, 87, 89, 90 and 96, as indicated. My comment: The difference in amino acid substitutions can be linked…

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Tet3 regulation of nutrient-dependent cell type differentiation

Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair was reported as: Neurons constantly rewrite their DNA Excerpt: “The scientists say they have discovered another mechanism used by neurons to maintain relatively consistent levels of synaptic activity so that neurons can remain responsive to the signaling around them. If synaptic activity increases, Tet3 activity and base excision of tagged cytosines increases. This causes the levels of GluR1 at synapses to decrease, in turn, which decreases their overall…

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Pathology constrains X-linked evolution

Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome Excerpt: “Experimental methods are already able to indicate the interactions between enhancers and genes8, 13, 17, 18, 19 but they are strongly constrained by the tissue and time where and when the interaction takes place. In contrast, evolutionary linkage is independent of the tissue or time of expression of the gene, and is applicable to any sequenced vertebrate genome, as it was done here for human.” My comment: Experimental…

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DNA Methylation and organized genomes

This open access review that is linked from the title (below) will appear in the next issue of Int J Biol Sci 2015; 11(5):604-617. doi:10.7150/ijbs.11218 It is a excellent, albeit incomplete, review of how nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions link the epigenetic landscape to the physical landscape of DNA via the biophysically constrained chemistry of cell type differentiation and the physiology of reproduction in all genera. The review is incomplete because they do not start with…

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A genetic variant refutes neo-Darwinism

Summary: They link a single nucleotide polymorphism (SNP) to a genetic variant that decreases viability of an embryo, without linking a nutrient-dependent RNA-mediated amino acid substitution to pheromone-controlled cell type differentiation that begins in the embryo and continues throughout the life history transitions of invertebrates and vertebrates. A Benefit of Failed Pregnancy? This genome-wide association study revealed “…a striking link between mitotic aneuploidy and a single nucleotide variant (SNP rs2305957) on chromosome 4 of maternal genomes.” Excerpt: “There’s this genetic…

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Methylation maintains cell type differences (2)

Follow up to:  Methylation maintains cell type differences Brain’s ‘gender’ may be quite flexible: Mechanism that plays key role in sexual differentiation of brain described Excerpt: “Prof. McCarthy is now doing additional research on the links between the immune system and brain sex differences.” See also: An immune hypothesis of sexual orientation Excerpt: “…this ICS-hypothesis is consistent with the fact that many mfTSs can have children and does not preclude effects of odors and pheromones, but elucidates why those substances…

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