Relative nucleosome preference of different subsets of synthetic 150-mers. (A) and (B) Dependence of relative nucleosome preference (as log2(occupancy ratio)) on G+C content (A) and maximum poly-A length (B). Oligonucleotides categorized as "Neutral %G+C" in (B) are those with 45-55% G+C. Graph below shows the frequency of the selected attribute in the oligonucleotides analyzed, and also the human and yeast genomes. (C) Dependence of relative occupancy on poly-A content and CpG status. Poly-A containing oligonucleotides are defined as containing at least four consecutive adenine bases. CpG oligonucleotides are defined as having a G+C content ≥50%, with an observed/expected CpG ratio ≥0.6 (Obs/Exp CpG = Number of CpG * N/(num G * num C), where N = length of sequence). The sequencing readout (rather than array readout) data from the Kaplan paper was used in this analysis. On all box plots, whiskers indicate 10th and 90th percentiles.
Tillo and Hughes BMC Bioinformatics 2009 10:442 doi:10.1186/1471-2105-10-442