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The log2 ratio of substitution rates of AT-to-GC (GC mutations) to that of GC-to-AT (AT mutations) was calculated as the index of substitution rate bias.
If AT mutations are segregating at higher frequency due to alignment errors, we would expect the pattern to be stronger in noncoding than coding regions.
However, it is difficult to understand why under this model AT mutations would occur at higher frequency on average, than GC mutations.
Several hundred ATM mutations have been identified in AT patients, most of which are heterozygous and inherit different AT mutations from each parent [ 9].
Careful analysis of the mutations reported in p53 mutation databases also provides corroborating evidence that the high incidence of GC > AT mutations in the p53 gene, observed in lung cancer, might also be related to non-CpG methylation, as well as to the overall increase of methylation sites in this locus.
Hodgkinia, somewhat mysteriously, shares in this universal bias toward AT mutations.
Similar(26)
These nupts have significantly accumulated GC-to-AT mutations, reflecting a nuclear mutational environment shaped by spontaneous deamination of 5-methylcytosin.
A recent study investigated specificity and rates of different mutational biases of the Salmonella typhimurium genome in the absence of major DNA repair systems [ 56], where mutator genes result in GC-to-AT mutations.
A more rigorous analysis is required to confirm whether the observed higher number of de novo GC-AT mutations [ 54, 55] are directly related to the loss of AT-increasing mutator genes.
Ultimately, GC-to-AT mutations are eliminated, whereas AT-to-GC ones are fixed in plastomes after gBGC (fig. 5), thus resulting in accumulation of GC-biased mutations.
In general, RIP induces GC-to-AT mutations in duplicated DNA sequences of more than 400 base pairs (bp) with sequence identity greater than 80% [ 18, 24].
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