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Demethylation: [...] removal of a methyl group (CH3) from a molecule. https://en.m.wikipedia.org/wiki/Demethylation https://en.m.wikipedia.org/wiki/Demethylatio

Demethylation: [...] removal of a methyl group (CH3) from a molecule. https://en.m.wikipedia.org/wiki/Demethylation https://en.m.wikipedia.org/wiki/Demethylation Is anyone familiar with this process and can explain this paper to me like I'm five? :)

nobodyknowsyoda 5y ago
Unfortunately don’t have time to check out the paper, but vaguely I am aware that methyl groups are like an accessory that can be attached or detached (by the cell, normally) to an arbitrary section of DNA within your chromosome. And it can be used in this way for regulation of DNA expression. Because when the methyl group is there it’s harder for that section of DNA to be read (transcribed) because the methyl group is physically in the way. The train can’t run on the track because there’s a big rock on it DNA is like code, but then there’s this whole meta level of DNA regulation that determines whether each section of code is used, and how much So by demethylizing some section of the DNA, implicitly that means the scientists made that section of DNA be used more often. And it just so happens that when that section of DNA is used more often it contributes to various processes that ultimately end up with the plant organism as a whole producing more “yield”, or parts of the plant that we like to eat https://en.m.wikipedia.org/wiki/DNA_methylation https://en.m.wikipedia.org/wiki/DNA_methylation
- credit_guy 5y ago
  Wow. Thanks for the explanation. It seems to me then that this result is a slam dunk Nobel. Yield improvement without the GMO stigma.
  - wolfretcrap 5y ago
    How is removing (obfuscation!?) smth from the DNA not genetic modification?
    - nwatson 5y ago
      In dealing with methylation one doesn't add to or remove the "code" to synthesize any particular protein from the cell(s) of the organism, the DNA/genes per se remains intact. The process inhibits / allows synthesis of particular proteins from the genes/DNA. Think of it like software -- by flipping an A/B Switch in software configuration you don't add to or remove from a program, you merely turn on/off certain features. Same with methylation -- it's the A/B Switch for protein synthesis, FWIU.
      - oh_sigh 5y ago
        I think most lay people would view this as genetic modification, or at least "genetic manipulation", which might be even scarier. Having said that, I'm pro-GMOs and always roll my eyes when brands go out of their way to say that they proudly don't use GMOs.
      - bawolff 5y ago
        Technically correct might be the best kind of correct, but i doubt it will change hearts and minds.
        adrianN 5y ago
        It's enough to circumvent regulations for marking products as GMO.
        bawolff 5y ago
        The EU definition is "organisms in which the genetic material (DNA) has been altered in a way that does not occur naturally by mating or natural recombination". https://publications.jrc.ec.europa.eu/repository/handle/JRC57223 https://publications.jrc.ec.europa.eu/repository/handle/JRC5... I'm honestly not sure which side of the definition this falls under. It certainly doesn't occur naturally.
        adrianN 5y ago
  - Scaevolus 5y ago
    This is GMO. They added a human gene to rice and potatoes to get the improved yields. People that dislike GMO aren't going to be any happier about adding _human_ genes to plants.
    - tingletech 5y ago
      As long as it’s not round up ready or otherwise encourage more pesticid use I’m cool with it
      - ncmncm 5y ago
        Or making the plant produce pesticide of its own, causing bugs to develop resistance to measures needed by organic farmers, and also dosing humans with what would otherwise be easily rinsed off.
    - shmageggy 5y ago
      I'm looking forward to the day when we can collectively disentangle GMO from all of the other negative practices of big ag. I don't see a reason why responsible genetic modification can't be a part of a sustainable and equitable future agricultural system.
      - londons_explore 5y ago
        "Genetically modifying food to increase yield is good for the environment" is a true statement, but you're going to need an awfully good PR firm to persuade the public it's true...
        shmageggy 5y ago
        Yeah exactly. And not only yield, but natural pest resistance, etc. I'm also imagining how genetic modifications might eventually be environmentally beneficial in the context of whole-ecosystem engineering if/when we ever move beyond a monocrop model, such as modifying native organisms to counter invasive species, etc. Admittedly a bit sci-fi currently but in principle possible!
- pazimzadeh 5y ago
  In this case it's RNA not DNA. Demethylating DNA is like uncommenting a line of code; demethylating RNA is like uncommenting compiled/assembly rather than the source.
  - eruleman 5y ago
    Thank you for this incredible analogy.
  - nobodyknowsyoda 5y ago
    Oops, thanks
KirillPanov 5y ago
I can't explain the paper, but if DNA is genetic ROM, methylation is like one bit of RAM available on each digit [*]. Most of the cellular machinery tries pretty damn hard to make exact copies of DNA. The methylation bits, by contrast, get deliberately flipped on and off all the time. [*] Technically only A and C can accept methylation, but in a double helix you'll always have either an A or a C on one side or the other at every position (A pairs with T, C pairs with G).
- trasz 5y ago
  Deliberately flipped based on what?
  - KirillPanov 5y ago
    That is an area of very active research. I mean the exact chemical mechanism for the flip is some enzyme, and the flip certainly affects gene expression. As to why the cellular systems flip these bits, great question :)

nobodyknowsyoda 5y ago

Unfortunately don’t have time to check out the paper, but vaguely I am aware that methyl groups are like an accessory that can be attached or detached (by the cell, normally) to an arbitrary section of DNA within your chromosome. And it can be used in this way for regulation of DNA expression. Because when the methyl group is there it’s harder for that section of DNA to be read (transcribed) because the methyl group is physically in the way. The train can’t run on the track because there’s a big rock on it DNA is like code, but then there’s this whole meta level of DNA regulation that determines whether each section of code is used, and how much So by demethylizing some section of the DNA, implicitly that means the scientists made that section of DNA be used more often. And it just so happens that when that section of DNA is used more often it contributes to various processes that ultimately end up with the plant organism as a whole producing more “yield”, or parts of the plant that we like to eat https://en.m.wikipedia.org/wiki/DNA_methylation https://en.m.wikipedia.org/wiki/DNA_methylation

credit_guy 5y ago
Wow. Thanks for the explanation. It seems to me then that this result is a slam dunk Nobel. Yield improvement without the GMO stigma.
- wolfretcrap 5y ago
  How is removing (obfuscation!?) smth from the DNA not genetic modification?
  - nwatson 5y ago
    In dealing with methylation one doesn't add to or remove the "code" to synthesize any particular protein from the cell(s) of the organism, the DNA/genes per se remains intact. The process inhibits / allows synthesis of particular proteins from the genes/DNA. Think of it like software -- by flipping an A/B Switch in software configuration you don't add to or remove from a program, you merely turn on/off certain features. Same with methylation -- it's the A/B Switch for protein synthesis, FWIU.
    - oh_sigh 5y ago
      I think most lay people would view this as genetic modification, or at least "genetic manipulation", which might be even scarier. Having said that, I'm pro-GMOs and always roll my eyes when brands go out of their way to say that they proudly don't use GMOs.
    - bawolff 5y ago
      Technically correct might be the best kind of correct, but i doubt it will change hearts and minds.
      - adrianN 5y ago
        It's enough to circumvent regulations for marking products as GMO.
        bawolff 5y ago
        The EU definition is "organisms in which the genetic material (DNA) has been altered in a way that does not occur naturally by mating or natural recombination". https://publications.jrc.ec.europa.eu/repository/handle/JRC57223 https://publications.jrc.ec.europa.eu/repository/handle/JRC5... I'm honestly not sure which side of the definition this falls under. It certainly doesn't occur naturally.
        adrianN 5y ago
- Scaevolus 5y ago
  This is GMO. They added a human gene to rice and potatoes to get the improved yields. People that dislike GMO aren't going to be any happier about adding _human_ genes to plants.
  - tingletech 5y ago
    As long as it’s not round up ready or otherwise encourage more pesticid use I’m cool with it
    - ncmncm 5y ago
      Or making the plant produce pesticide of its own, causing bugs to develop resistance to measures needed by organic farmers, and also dosing humans with what would otherwise be easily rinsed off.
  - shmageggy 5y ago
    I'm looking forward to the day when we can collectively disentangle GMO from all of the other negative practices of big ag. I don't see a reason why responsible genetic modification can't be a part of a sustainable and equitable future agricultural system.
    - londons_explore 5y ago
      "Genetically modifying food to increase yield is good for the environment" is a true statement, but you're going to need an awfully good PR firm to persuade the public it's true...
      - shmageggy 5y ago
        Yeah exactly. And not only yield, but natural pest resistance, etc. I'm also imagining how genetic modifications might eventually be environmentally beneficial in the context of whole-ecosystem engineering if/when we ever move beyond a monocrop model, such as modifying native organisms to counter invasive species, etc. Admittedly a bit sci-fi currently but in principle possible!
pazimzadeh 5y ago
In this case it's RNA not DNA. Demethylating DNA is like uncommenting a line of code; demethylating RNA is like uncommenting compiled/assembly rather than the source.
- eruleman 5y ago
  Thank you for this incredible analogy.
- nobodyknowsyoda 5y ago
  Oops, thanks

KirillPanov 5y ago

I can't explain the paper, but if DNA is genetic ROM, methylation is like one bit of RAM available on each digit [*]. Most of the cellular machinery tries pretty damn hard to make exact copies of DNA. The methylation bits, by contrast, get deliberately flipped on and off all the time. [*] Technically only A and C can accept methylation, but in a double helix you'll always have either an A or a C on one side or the other at every position (A pairs with T, C pairs with G).

trasz 5y ago
Deliberately flipped based on what?
- KirillPanov 5y ago
  That is an area of very active research. I mean the exact chemical mechanism for the flip is some enzyme, and the flip certainly affects gene expression. As to why the cellular systems flip these bits, great question :)