Transposons: crossroads, crosstalk and gene regulation

By: James V. Kohl | Published on: March 5, 2020

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The energy-dependent space-time continuum links Creation of the sense of smell in bacteria to our visual perception of energy and mass via Olfaction Warps Visual Time Perception. That fact may require National Parks to revise their claims about evolution across billions to millions of years.

See:

At 10:22, the claim is stated that:

…shallow valleys of limestone that have been eroded over the past 5000 years

That claim links the middens of the earliest inhabitants, about 4,500 years ago, to what is known about the energy-dependent physiology of reproduction in Geobacter and to sympatric speciaton in periphyton.

For comparison to across-kingdom sympatric speciation from Geobacter to periphyton, you can see how shotgun genomics was used to misrepresent the age of pack-rat ecosystems via their middens. Theorists theorists claim the middens are from 300 to 48,000 years old in Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA 2/20/20
Warning: Some paleoecologists link C14 dating to claims about paleo-metagenomics and the age of middens by starting with claims from other biologically uninformed theorists. The theorists tend to start with ancient DNA. Their claims can be compared to the claims of serious scientists who have linked God’s Creation of sunlight and water to oxygen-dependent biophysically constrained viral latency via light-activated carbon fixation and RNA interference.
For instance, the patent for naturally occurring light-activated carbon fixation and RNA interference links biophysically constrained viral latency to healthy ecosystems in all living genera.
See: RNA-Guided Human Genome Engineering

5. Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

See for contrast: Crossroads between transposons and gene regulation

Transposons are mobile genetic elements that have made a large contribution to genome evolution in a largely species-specific manner. A wide variety of different transposons have invaded genomes throughout evolution…

The assumption that invaded genomes evolve has never been supported by experimental evidence of top-down causation. Top-down causation is energy-dependent and microRNA-mediated via light-activated carbon fixation, which biophysically constrains RNA interference.

See: Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes

Eukaryotic gene regulation is mediated by cis-regulatory elements, which are embedded within the vast non-coding genomic space and recognized by the transcription factors in a sequence- and context-dependent manner.

Gene regulation is energy-dependent and energy is linked to their claim about the context-dependent manner.

See: An atlas of transposable element-derived alternative splicing in cancer

Transposable element (TE)-derived sequences comprise more than half of the human genome, and their presence has been documented to alter gene expression in a number of different ways, including the generation of alternatively spliced transcript…

Energy is required for the generation of alternatively spliced transcripts. The senior author, I. King Jordan should know that. No serious scientists took his claims seriously when he wrote: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
Similarly, genomic responses do not evolve. See: Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster

Most of the genotype–phenotype analyses to date have largely centred attention on single nucleotide polymorphisms. However, transposable element (TE) insertions have arisen as a plausible addition to the study of the genotypic–phenotypic link.

The genotypic–phenotypic link is energy-dependent and biophysically constrained by the physiology of reproduction. Everything known about the genotypic–phenotypic link requires the energy-dependent Creation of enzymes.
See: KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity

KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation, notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes

Proteins do not automagically Create themselves and neither do actively expressed genes. What then can be said about theorists who skip the energy-dependent creation of enzymes and make claims about ‘junk’ DNA, evolved species or other neo-Darwinian pseudoscientific nonsense?

See: On transposons and totipotency

Our perception of the role of the previously considered ‘selfish’ or ‘junk’ DNA has been dramatically altered in the past 20 years or so. A large proportion of this non-coding part of mammalian genomes is repetitive in nature…

The plant-specific RNA Polymerase IV (Pol IV) transcribes heterochromatic regions, including many transposable elements (TEs), with the well-described role of generating 24 nucleotide (nt) small interfering RNAs (siRNAs). These siRNAs target DNA

Are any neo-Darwinian theorists using the right tools and techniques to elaborate on energy-dependent biophysically constrained gene regulation?
See: Mobile genomics: tools and techniques for tackling transposons

Next-generation sequencing approaches have fundamentally changed the types of questions that can be asked about gene function and regulation. With the goal of approaching truly genome-wide quantifications of all the interaction partners…

All the interaction partners are energy-dependent and microRNA-mediated.

But see: Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns

The large family of KRAB zinc finger (KZNF) genes are transcription factors implicated in recognizing and repressing repetitive sequences such as transposable elements (TEs) in our genome. Through successive waves of retrotransposition-mediated…

When did energy-dependent microRNA-mediated gene regulation become retrotransposition-mediated and/or SINE-mediated?

See: Short interspersed nuclear element (SINE)-mediated post-transcriptional effects on human and mouse gene expression: SINE-UP for active duty

This review describes how human cells have used 3′UTR Alu elements to mediate post-transcriptional gene regulation and also describes examples of convergent evolution between human and mouse 3′UTR SINEs.

The review fails to link energy-dependent changes in the microRNA/messenger RNA balance to biophysically constrained viral latency via the mouse-to-human model of EDAR V370A fixation. To her credit, Lynne E. Maquat claims that rodent-specific B and ID (B/ID) SINEs are non-autonomous, which suggests the short interspersed nuclear element (SINE)-mediated post-transcriptional effects on human and mouse gene expression are energy-dependent in all living genera.
All claims about convergent evolution between humans and mice can be reexamined in the context of: Insertion of 60 homing guide RNA (hgRNA) loci in locations scattered throughout the genome.
See: Genetic Alterations
Note: The mouse strain used for this research project, STOCK MARC1-PB7/Mmucd, RRID:MMRRC_065424-UCD, was obtained from the Mutant Mouse Resource and Research Center (MMRRC) at University of California at Davis, an NIH-funded strain repository, and was donated to the MMRRC by George M. Church, Ph.D., Harvard Medical School and Reza Kalhor, Ph.D., Harvard Medical School.

This mouse line is called “Mouse For Actively Recording Cells!” or MARC1. It is used for barcoding and lineage tracing applications in the mouse, as described in the referenced publications. The line does not have a disease phenotype. However, when a MARC1-PB7 mouse is crossed to mice expressing cas9 universally or in a lineage-specific manner, combinatorial and cumulative barcoding starts in the progeny during their development, leading to developmentally barcoded animals that can be used for a multitude of applications, including lineage tracing.

That facts ab0ut lineage tracing are consistent with what is known to serious scientists about the energy-dependent links to the regulation of bacterial infections.
See: Transposable elements have contributed human regulatory regions that are activated upon bacterial infection

Transposable elements (TEs) are increasingly recognized as important contributors to mammalian regulatory systems. For instance, they have been shown to play a role in the human interferon response…

RNA silencing is a posttranscriptional gene silencing mechanism directed by endogenous small non-coding RNAs called microRNAs (miRNAs). By contrast, the type-I interferon (IFN) response is an innate immune response induced by exogenous RNAs, such as viral RNAs. Endogenous and exogenous RNAs have typical structural features and are recognized accurately by specific RNA-binding proteins in each pathway. In mammalian cells, both RNA silencing and the IFN response are induced by double-stranded RNAs (dsRNAs) in the cytoplasm, but have long been considered two independent pathways. However, recent reports have shed light on crosstalk between the two pathways, which are mutually regulated by protein-protein interactions triggered by viral infection. This review provides brief overviews of RNA silencing and the IFN response and an outline of the molecular mechanism of their crosstalk and its biological implications. Crosstalk between RNA silencing and the IFN response may reveal a novel antiviral defense system that is regulated by miRNAs in mammalian cells.

Theorists tend to skip the facts about the crosstalk between the two pathways and skip the facts about energy-dependent microRNA-mediated biophysically contrained viral latency.
See: Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

Long interspersed element-1 (LINE-1, L1) sequences, which comprise about 17% of human genome, are the product of one of the most active types of mobile DNAs in modern humans. LINE-1 insertion alleles can cause inherited and de novo genetic diseases

Claims about inherited and de novo genetic diseases elicit ridicule from serious scientists who know that supercoiled DNA does not create itself.
See: Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling.

See for comparison: Contribution of unfixed transposable element insertions to human regulatory variation

Thousands of unfixed transposable element (TE) insertions segregate in the human population, but little is known about their impact on genome function. Recently, a few studies associated unfixed TE insertions to mRNA levels of adjacent genes…

The levels of biological organization linked to mRNA levels of adjacent genes link the pheromone-controlled physiology of reproduction in soil bacteria to biophysically contrained RNA interference in plants and mammals.

See:Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare)

In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs).

L1 activity has generated at least a third of the human genome during evolution, and RC- L1s, Alus and SVAs continue to impact our genome.

The links from RNA interference to biophysically constrained viral latency and all biodiversity can also be placed into the context of what theorists call virus evolution.

Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

Koel et al. (p. 976) show that major antigenic change can be caused by single amino acid substitutions.

The single amino acid substitutions link ecological variation to ecological adaptations via changes in enzymes that cause changes in the microRNA/messenger RNA balance.
See for an example of how the changes are linked to adaptations in neurons:
Hypoxia-induced apoptosis of Astrocytes is mediated by reduction of Dicer and activation of caspase-1 3/4/20

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Transposons: crossroads, crosstalk and gene regulation

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