Gradualism in Evolution: the role of transposons (Agnosticism)

by David Turell , Tuesday, February 09, 2021, 22:32 (1382 days ago) @ David Turell

They are everywhere in genomes and advance evolution:

https://phys.org/news/2021-02-virally-derived-transposons-domesticated-evolve.html

"About half of our genome is made up of transposable elements (TEs), also known as transposons. These 'jumping genes' are short stretches of DNA that have the unique ability to duplicate themselves and change their position within our code. While these philanderings play an essential role in the evolution of the species, if unchecked, transposons can wreak havoc on the genome.

"Although the transcription and proliferation of TEs is usually constrained by DNA methylation or other repressive chromatin amendments, TEs sometimes escape these countermeasures. For example, at certain periods of germ cell gametogenesis and early embryonic development, many epigenetic controls are wiped clean during scheduled system-wide reboots. Fortunately, cells have a backup mechanism known as the PIWI/piRNA pathway which can repress TEs. A recent paper in Nature Reviews Molecular Cell Biology investigates the many ways in which piRNAs can silence TEs, and defines new mechanisms by which they might also control gene expression.

"In the PIWI/piRNA pathway, RNA molecules about 25-32 nucleotides long associate with the Argonaute proteins from the PIWI clade to form piRISC complexes. These complexes target TEs post-transcriptionally, and also through the induction of epigenetic changes at the loci from which they are expressed. Piwi is an abbreviation of "P-element Induced WImpy testis," with the "P" meaning paternal.

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"Two main classes of TEs can be defined. Class I TEs are called retrotransposons, which generally function via reverse transcription of the DNA into an RNA intermediate, hinting at their retroviral ancestry. Retrotransposons are commonly grouped into three main orders of decreasing size and complexity; the retrotransposons with long terminal repeats (LTRs), the LINES (which have reverse transcriptase but not LTRs), and the SINEs (which have neither). Class II TEs are the DNA transposons, which typically encode several sequence curiosities including a special transposase used for insertion and excision.

"Lest we give the impression that the transposon hazard is something we should be better off without, consider that transposons are solely responsible for most, or at least many, of the higher evolutionary refinements we enjoy today. Everything from live birth to expansion of the neocortex appears to have been driven by genome-wide insertion of TEs into the promoter regions of key regulatory genes. No other evolutionary process capable of radically altering the expression of so many genes in such a short time has been identified, let alone imagined. (my bold)

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"The magic sauce hidden in these transposable elements is that they happen to be good at creating transcription factor binding sites."

Comment: The article contains many specific types of genetic activity conducted by these TE's. Is this God's supreme method for advancing evolution?