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Are gene conversions and expansion/contraction of repetitive (satellite) DNA examples of directional, non-random mutations? For some context, it was brought to mind as a result of reading the following;

"Within the broad category of gene mutations we should consider not only the classical, purportedly random changes, but also the internally directed changes that are called gene conversion and duplicative transposition (collectively constituting molecular drive) (see Dover et al., 1981)." (From 'A Botanical Critique of Cladism', pp 14-15)

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  • $\begingroup$ Please include your question in the question. A title is a title. This will also make you explain more fully and clearly. $\endgroup$
    – David
    Commented Sep 19, 2022 at 16:43

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For Repetitive Sequences:

Duplications of repetitive DNA (as in replication-slippage) are not "as random" as radioactivity, but still, there is no genetic mechanism that intentionally triggers the duplication of a gene. Also, during replication slippage the site of DNA-pol re-association is random, causing duplications of different lengths. So I'd still call it a change that's both "random" (in terms of sequence) and "non directed" (as in "lacks a direct purpose").

Together, I'd prefer the term "duplication" over "mutation" for the expansion of repetitive/satellite DNA, (while "duplication" is a type of "mutation")

For Transposons:

Your reference cites 'duplicative transposition', and a lot of repetitive DNA originate from transposons (Belyayev 2020). For jumping genes, I would prefer the term „recombination“ instead of "mutation".

The appearance/exchange of specific large sequences is called Recombination.

From Harret & Sherrat 1997:

In bacteria, two categories of specialised recombination promote a variety of DNA rearrangements. Transposition is the process by which genetic elements move between different locations of the genome, whereas site-specific recombination is a reaction in which DNA strands are broken and exchanged at precise positions of two target DNA loci to achieve determined biological function. Both types of recombination are represented by diverse genetic systems which generally encode their own recombination enzymes. These enzymes, generically called transposases and site-specific recombinases […].

Furthermore, so it‘s incorrect to categorize transposons as „non-random“, since they insert mostly at random sites and can cause random DNA-damage next to the excision/insertion site Wicker et al. 2016.

Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions.

In my eyes, a better example of "directed"/"intended" (but random in sense of sequence) mutagenesis would be AID, an enzyme that increases antibody binding variability by intentionally introducing point mutations at very specific and isolated sites inside one gene.

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  • $\begingroup$ I can see how AID increases genome-wide mutation rates, but the individual mutations are still 'random' in the sense that there's no bias towards a specific sequence appearing at any site in the genome. On the other hand, it would appear to me that slippage at repetitive sites, and gene conversions (transpositions too though I didn't mention them), bias the appearances of specific sequences in the genome. $\endgroup$
    – arara
    Commented Sep 19, 2022 at 17:23
  • $\begingroup$ AID does not act genome wide. It‘s directed towards the variable region of immunoglobulin genes where it introduces random mutations in an isolated section in a controlled manner. You are mistaken, Transposons are not specific. They can even insert inside genes an inactivate them, and if too many transposons are active, they will destabilize the genome (see piRNAs and infertility). In general, when talking about mutation, geneticists don‘t immediatley think about transposons. A far better term for large sequences changing location would be „recombination“ $\endgroup$
    – markur
    Commented Sep 19, 2022 at 20:15
  • $\begingroup$ Understood for immunoglobin genes although the same point applies, the 'gene-wide' mutation rate doesn't bias the appearance of specific sequences or nucleotides (or does it?). I was not saying transposon insertion sites is non-random: what's non-random is the appearance of sequences specifically corresponding to the transposon sequence. $\endgroup$
    – arara
    Commented Sep 20, 2022 at 1:22
  • $\begingroup$ Yes, but the appearance of specific large sequences is better described with the term „recombination“ than with „mutation“. Yes, the term mutation is associated with transposons, BUT the mutation from transposon is due to random errors that come with sloppy deletion/integration of the transposon and subsequent DNA-repair (and not due to appearance of large specific sequences) Wicker et al. 2016. $\endgroup$
    – markur
    Commented Sep 20, 2022 at 7:03
  • $\begingroup$ Yeah, it makes sense to better describe it as recombination. What about expansion/contraction of repetitive DNA and gene conversions? Do you agree that this is directional mutation when it comes to appearance of specific sequences or do you think this is still, technically, random? $\endgroup$
    – arara
    Commented Sep 20, 2022 at 15:15

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