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• W2975008049 abstract "Abstract Background Coding DNA in eukaryotes shows a prominent periodicity at 3–base pair (bp) because of the nonuniform use of bases at the three codon positions. This periodicity can also be interpreted as a correlation between bases at a distance of 3–bp, which in turn implies enhanced predictability at that distance as well as at integer multiples of 3 bp. This study examined possible similar dependencies between nucleotide positions in human promoter region sequences. It is possible that such noncoding sequences might show enhanced predictability at various distances other than 3 bps because of the ubiquitousness of repetitive patterns such as Short Tandem Repeats (STR). It is also possible that the 3D conformational requirements of helical DNA could induce a dependency between bps occupying certain relative positions. Mutual Information (MI), an information–theoretic quantity that can be interpreted as a measure of correlation or predictability between two sequence positions, was used to probe promoter sequences in Homo sapiens. Coding DNA sequences were also probed as a methodological control. Results The MI measure showed a clear 3–bp signal with integer harmonics in coding DNA sequences. This shows that the MI measure is sensitive to a known repetitive signal in coding DNA sequences. MI in promoter sequences fell with increasing distance between two positions, but also showed an unexpected and significant rise at a distance of 6–bp (i.e., between the first and the seventh bases in a sequence). Harmonic intrusion of a 3–bp signal from coding DNA was ruled out as an explanation for this 6–bp signal in promoter DNA. Purposely misaligning the promoter sequences had essentially no effect on the increased correlation at a distance of 6 bp. Conclusions Human promoter DNA sequences shows enhanced predictability (i.e., increased mutual information) between a given position and a position 6 bp downstream. This signal runs counter to the general fall in mutual information as the distance between positions increases. The increased correlation at a distance of 6 bp does not depend on the precise alignment of the sequences. Possible explanations for this enhanced predictability are discussed." @default.
• W2975008049 created "2019-10-03" @default.
• W2975008049 creator A5030957997 @default.
• W2975008049 date "2019-09-30" @default.
• W2975008049 modified "2023-09-23" @default.
• W2975008049 title "Mutual Information Reveals a 6 Base Pair Signal in Noncoding DNA" @default.
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