[HN Gopher] Scientists Catch Jumping Genes Rewiring Genomes
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       Scientists Catch Jumping Genes Rewiring Genomes
        
       Author : nsoonhui
       Score  : 69 points
       Date   : 2021-05-13 10:07 UTC (12 hours ago)
        
 (HTM) web link (www.quantamagazine.org)
 (TXT) w3m dump (www.quantamagazine.org)
        
       | ak217 wrote:
       | >For more than a decade, Feschotte has pointed to transposons as
       | the ultimate innovators in eukaryotic genomes.
       | 
       | To be clear, there is a long history of scientific theories and
       | studies on how transposable elements are key to eukaryotic genome
       | evolution, regulatory network formation and genome plasticity,
       | predating the review linked in that sentence - in fact, dating
       | all the way back to Barbara McClintock. I would call this an
       | under-studied area of genomics - I think there are still quite a
       | few Nobel prizes to be made in transposon-mediated evolution.
       | 
       | The new Feschotte article
       | (https://science.sciencemag.org/content/371/6531/eabc6405)
       | demonstrates a transcription factor in bats and uses a reporter
       | assay to link it to signatures of transposon activity, and also
       | uses comparative genomics to identify lineage-specific signatures
       | of transposon activity in tetrapods. This is a big step forward,
       | especially in using reporter assays to link TE activity to TF
       | networks in mammals, but I think the next step would be to do
       | both the in silico and the in vitro experiment together (use a
       | reporter assay to prove that lineage-specific regulatory network
       | patterns are linked to transposon activity).
        
         | dnautics wrote:
         | also transposons certainly exist in prokarya too, and probably
         | drive innovation there as well, possibly assisting horizontal
         | gene transfer. When I was in the synthetic genome lab at the
         | venter institute, one of the first things I did was win a bet
         | about the orientation of a transposable element in the syn1.0
         | genome that was eventually removed from the genome (the bet was
         | not important enough to merit me being on the paper)
        
       | f6v wrote:
       | > Pax6 is only one of thousands of genes encoding transcription
       | factors
       | 
       | Last time I checked humans only had ~1800 TFs. I don't know about
       | "thousands". Maybe if we count all TFs in all organisms excluding
       | homologs...
       | 
       | > While geneticists have made leaps in understanding how genes
       | with relatively simple, direct functions could have evolved,
       | explanations for transcription factors have largely eluded
       | scientists.
       | 
       | Is it that much different though? TFs bind short DNA sequences
       | throughout the genome. These sequences don't have to be exact,
       | some variation is allowed. Now, random mutations can change the
       | DNA and enable TF binding, thus increasing the fitness(since TF
       | increasing or decreasing expression of a gene can give some
       | advantage).
        
         | ak217 wrote:
         | A transcription factor gene regulatory network is much more
         | likely to arise through gene duplication and upstream
         | transposon insertions than by random mutation - especially in
         | plants and animals, which have long generation times, low
         | population sizes, and proofreading processes to suppress point
         | mutations, while also facilitating gene duplication via sexual
         | recombination. Eukaryotes have also evolved chromatin
         | accessibility restrictions to control not just expression but
         | evolvability of DNA regions. Point mutations on their own don't
         | seem like a plausible mechanism for the level of plasticity
         | exhibited in plant and animal genomes.
        
       | UncleOxidant wrote:
       | A bit of an aside, but I'm wondering if anyone is applying some
       | of these ideas to genetic algorithms?
        
         | ptrott2017 wrote:
         | Leonid Zamdborg et al published a good paper on this a few
         | years ago and it has a very good overview of related previous
         | work. All the referenced papers in the background and related
         | works section are all worth reading:
         | 
         | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353400/
        
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       (page generated 2021-05-13 23:02 UTC)