• New DNA modification system discovered i

    From ScienceDaily@1:317/3 to All on Mon Feb 28 21:30:40 2022
    New DNA modification system discovered in animals, captured from
    bacteria more than 60 MYA

    Date:
    February 28, 2022
    Source:
    Marine Biological Laboratory
    Summary:
    In humans and other eukaryotes, two principal epigenetic marks
    are known.

    A team has discovered a third, novel epigenetic mark -- one
    formerly known only in bacteria -- in bdelloid rotifers, small
    freshwater animals.

    Epigenetic marks are modifications to DNA bases that don't change
    the underlying genetic code, but 'write' extra information on top
    of it that can be inherited along with your genome.



    FULL STORY ==========================================================================
    Your DNA holds the blueprint to build your body, but it's a living
    document: Adjustments to the design can be made by epigenetic marks.


    ========================================================================== Epigenetic marks are modifications to DNA bases that don't change the underlying genetic code, but "write" extra information on top of it that
    can be inherited along with your genome. Epigenetic marks usually regulate
    gene expression -- turn genes on or off -- particularly during early development or when your body is under stress. They can also suppress
    "jumping genes" - - transposable elements that threaten the integrity
    of your genome.

    In humans and other eukaryotes, two principal epigenetic marks are
    known. A team from the Marine Biological Laboratory (MBL) has discovered
    a third, novel epigenetic mark -- one formerly known only in bacteria --
    in bdelloid rotifers, small freshwater animals. This fundamental and
    surprising discovery is reported this week in Nature Communications.

    "We discovered back in 2008 that bdelloid rotifers are very good at
    capturing foreign genes," said senior author Irina Arkhipova, senior
    scientist in the MBL's Josephine Bay Paul Center. "What we've found here
    is that rotifers, about 60 million years ago, accidentally captured
    a bacterial gene that allowed them to introduce a new epigenetic mark
    that was not there before." This is the first time that a horizontally transferred gene has been shown to reshape the gene regulatory system
    in a eukaryote.

    "This is very unusual and has not been previously reported," Arkhipova
    said.

    "Horizontally transferred genes are thought to preferentially be
    operational genes, not regulatory genes. It is hard to imagine how a
    single, horizontally transferred gene would form a new regulatory system, because the existing regulatory systems are already very complicated."
    "It's almost unbelievable," said co-first author Irina Yushenova, a
    research scientist in Arkhipova's lab. "Just try to picture, somewhere
    back in time, a piece of bacterial DNA happened to be fused to a piece
    of eukaryotic DNA. Both of them became joined in the rotifer's genome
    and they formed a functional enzyme. That's not so easy to do, even in
    the lab, and it happened naturally.

    And then this composite enzyme created this amazing regulatory system,
    and bdelloid rotifers were able to start using it to control all these
    jumping transposons. It's like magic." "You don't want transposons
    jumping around in your genome," said first author Fernando Rodriguez,
    also a research scientist in Arkhipova's lab. "They will mess things up,
    so you want to keep them in check. And the epigenetic system to accomplish
    that is different in different animals. In this case, a horizontal gene transfer from bacteria into bdelloid rotifers created a new epigenetic
    system in animals that hasn't been described before."


    ========================================================================== "Bdelloid rotifers, especially, have to keep their transposons in check
    because they primarily reproduce asexually," Arkhipova said. "Asexual
    lineages have fewer means for suppressing proliferation of deleterious transposons, so adding an extra layer of protection could prevent a
    mutational meltdown. Indeed, transposon content is much lower in bdelloids
    than it is in sexual eukaryotes that don't have this extra epigenetic
    layer in their genome defense system." In the two previously known
    epigenetic marks in eukaryotes, a methyl group is added to a DNA base,
    either cytosine or adenine. The team's newly discovered mark is also a
    cytosine modification, but with a distinct bacterial-like positioning
    of the methyl group -- essentially recapitulating evolutionary events
    of over two billion years ago, when the conventional epigenetic marks
    in early eukaryotes emerged.

    Bdelloid rotifers are extremely resilient animals, as the Arkhipova and
    David Mark Welch labs at MBL have discovered over the years. They can completely dry up (desiccate) for weeks or months at a time, and then
    spring back to life when water becomes available. During their desiccation phases, their DNA breaks up into many pieces. "When they rehydrate or
    otherwise render their DNA ends accessible, this might be an opportunity
    for foreign DNA fragments from ingested bacteria, fungi, or microalgae
    to transfer into the rotifer genome," Arkhipova said. About 10 percent
    of the rotifer genome comes from non-metazoan sources, they have found.

    Still, the Arkhipova lab was surprised to find a gene in the rotifer
    genome that resembled a bacterial methyltransferase (a methyltransferase catalyzes the transfer of a methyl group to DNA). "We hypothesized that
    this gene conferred this new function of suppressing transposons, and we
    spent the last six years proving that, indeed, it does," Arkhipova said.

    It's too early to know what the implications may be of discovering this
    new epigenetic system in rotifers. "A good comparison is the CRISPR-Cas
    system in bacteria, which started out as a basic research discovery. Now CRISPR-Cas9 is used everywhere as a tool for gene editing in other
    organisms," Rodriguez said.

    "This is a new system. Will it have applications, implications for
    future research? It's hard to tell." These discoveries open the door
    to new tools and research directions to investigate genome function and resilience in this rotifer system. In the future, such knowledge may be
    applied in creative ways to impact ssociety during this time of rapid environmental change.

    ========================================================================== Story Source: Materials provided by Marine_Biological_Laboratory. Original written by Diana Kenney. Note: Content may be edited for style and length.


    ========================================================================== Related Multimedia:
    * Bdelloid_rotifer ========================================================================== Journal Reference:
    1. Fernando Rodriguez, Irina A. Yushenova, Daniel DiCorpo, Irina R.

    Arkhipova. Bacterial N4-methylcytosine as an epigenetic mark
    in eukaryotic DNA. Nature Communications, 2022; 13 (1) DOI:
    10.1038/s41467- 022-28471-w ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/02/220228091140.htm

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