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CpG islands are regions with an high frequency of CpG (Cytosine-phosphate-Guanine) sites. The usual formal definition is that of a region with at least 200 bp, a GC percentage greater than 50% and an observed to expected ratio grater than 60%. In colorectal cancer, these regions have been found drastically methylated with respect to the normal mucosa tissues surrounding the tumor (Illingworth et al. 2010). This brought to speculate a role in the cancer onset. My question is: are there any other kind of dinucleotide rich regions that represent important cases of study in literature?If yes, can you suggest me some papers and references?Than you

Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP (2010). "Orphan CpG islands identify numerous conserved promoters in the mammalian genome". PLOS Genet. 6 (9): e1001134. doi:10.1371/journal.pgen.1001134. PMC 2944787. PMID 20885785.

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In some types of cancers like breast cancer, APOBEC3 cytidine deaminases can become upregulated and enhance mutagenesis. As shown in this mutational signature from cancer tissue data the enzymes prefer TC motifs. APOBEC Mutation Signature Source: https://cancer.sanger.ac.uk/cosmic/signatures/SBS/index.tt

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  • $\begingroup$ Are there signatures in protozoans or in micro-organisms (Eukaryota)?By your experience, to find a huge proportion with respect to the gene length,of TC motifs or TT motifs, could be representative of the proclivity of a protein coding gene to undergo cross-linkings or, in general, sufficient to speculate such a tendency?Given the degeneracy of the genetic code I am restrained to assume such a conclusion (a lot of codons with TC and TT in their first and second codon position)and I am asking for that $\endgroup$
    – Spartan 117
    Oct 19, 2020 at 17:02
  • $\begingroup$ This particular signature no, unless you introduce an APOBEC3 gene into that species and there are labs that have recreated this signature in yeast using mammalian genes. There are other signatures with no known etiology or suspected to be environmental (UV, reactive oxygen species, etc.) that one would expect in other eukaryotes and there are labs that study this. I don't know about your gene question. Mutation signatures are created from genome wide sequencing and I don't know if anyone has looked at local chromosome structure. $\endgroup$
    – user40950
    Oct 19, 2020 at 17:27
  • $\begingroup$ Anyway, your suggestion are greatly appreciated. $\endgroup$
    – Spartan 117
    Oct 19, 2020 at 18:12
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The obvious answer (to me) is dinucleotide microsatellites, though it may not make sense to restrict to dinucleotides unless you had some particular reason; other motifs (e.g. mononucleotide repeats) have higher mutation rates. It also depends to some extent on the organism.

While the particular motif may have only a modest effect on mutation rate (e.g. Figure S9 here), microsatellites in general have very high mutation rates and certainly have a nonrandom distribution pattern throughout genomic regions that have functional effects.

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