Location of Putative Quadruplexes

Using the ENSEMBL database, it is possible to classify regions of the genome as related to genes. This information was used to investigate the number of 

These results break the pseudo-ChargafF rule observed in the rest of the genome - G and C do not behave similarly, and nor do A and T. This can occur because the two DNA strands are distinct in exonic regions, with only one of them being transcribed to form RNA. However, that does not explain why such a marked decrease in G-patterns is observed. 

One possible explanation is the simple observation that the G-rich codons do not code for the same amino acids as C-rich codons, but modelling based on codon frequencies shows that the predicted discrimination from this alone is not sufficient to account for the observation. An alternative explanation is based on the observation that the G-patterns would lead to potential quadruplexes in the mRNA strand in addition to the DNA duplex, whereas C-patterns could only lead to quadruplexes in the (complementary strand of) DNA. This evidence is consistent with an evolutionary pressure to reduce the number of quadruplexes allowed to form in mRNA. This may be particularly strong as it seems that RNA quadruplexes are more stable, both thermodynamically and kinetically, than their DNA counterparts. To date, there has been relatively little work focused on RNA quadruplexes, although it has evoked some interest. However these results suggest that RNA quadruplexes could play a significant physiological role, and should be investigated further. 

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