Mutual information reveals a homonucleotide bias at 6 bp distance in promoters

Motivation Statistical dependencies between nucleotides at different positions within a DNA sequence have been used for several purposes including distinguishing coding from noncoding regions of a genome. Coding sequences show correlations within and between codon positions. This study asked whether such correlations between positions separated by short distances might also exist in noncoding DNA. To this end, positional nucleotide dependencies were examined in the promoter regions of four eukaryotic species: Homo sapiens ( Hs ), Mus musculus ( Mm ), Drosophila melanogaster ( Dm ), and Saccharomyces cerevisiae ( Sc ). The degree of dependency between pairwise positions across a set of aligned sequences was quantified by Mutual Information (MI) and visualized using a novel heatmap method. Results MI in promoter sequences aligned at their putative Transcription Start Site (TSS) generally decreased with increasing distance between two positions, but also showed a prominent increase at a distance of 6 base pairs (bp) (i.e., between nucleotides at x and x + 6 in a sequence) in the three multicellular species, but much less so in Sc . This dependency at a distance of 6 bp appears to reflect an N 1 … N 7 homonucleotide bias in promoters. Availability R code and data files available at github/dannemil/promoters. Contact [email protected] Supplementary information Dannemiller-supplementary-documents . zip