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  • CG dinucleotide frequency

    I just made an amazing discovery : the content of CG-binucleotides
    in human DNA is much lower (~one fourth) of the content of other
    binucleotides, e.g. GC.
    This is so basic, fundamental, that it must be known and there should
    be a keyword where/how to find more about it ?!
    But I never saw it.

    The ratio (number of GC)/number of CG) seems to depend on
    chromosome-length, it's also seen in other vertibrates,
    average ratio maybe 2 ,
    not in invertibrates,viruses, bacteria where I got a ratio of ~1.2,
    except HIV with 5.8(!) , influenza with 2.2

    hepatitis with 1.35 , oryza 1.39 , gallus 5.0 , influenza-B 2.8
    human mitochondrial DNA 1.63
    human chr01:4.36
    human chr22:3.44


    so, how is this phenomenon called ? Where to find more about it ?
    is it because the assembling of CG takes longer and is thus avoided ?


    human chromosome 1:
    AA,21387422
    AC,11301414
    AG,16036982
    AT,16766098
    CA,16363109
    CC,12259077
    CG, 2281713
    CT,16060830
    GA,13448131
    GC, 9938922
    GG,12248730
    GT,11320734
    TA,14293281
    TC,13465343
    TG,16389034
    TT,21438891

    GC/CG-ratio=4.355904

    --------------------------------------------------

    OK, I found the answer now myself : "DNA-methylation"

    ----------------------------------------------------
    Last edited by gsgs; 03-31-2013, 06:11 AM.

  • #2
    Look for CpG islands and methylation. My understanding is that CG dinucleotides are selected against because they are prone to methylation with subsequent deamination.

    Comment


    • #3
      thanks. Why is the ratio bigger in longer chromosomes ?

      -------------edit--------------
      DNA methylation is not found in all species.
      It is absent or extremely rare in invertebrates such as
      Drosophila and Caenorhabditis elegans, whereas it has
      been found in sponges, some insects, sea urchins, and
      invertebrate chordates, as well as in all vertebrates and
      plants so far examined. (1998)
      -----------------------------------
      Last edited by gsgs; 07-03-2013, 07:40 AM.

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