Figure 5

Sequence-based nucleosome-binding preferences in P. falciparum . A-B. Frequency of AA + TT and GG + CC dinucleotides in nucleosome-bound DNA fragments in coding regions (A) and intergenic regions (B). For nucleosomes located inside genes, a weak 10 bp periodicity was observed directly internal to the nucleosome boundaries, but disappearing closer to the nucleosome dyad. C-D. Enrichment of 5-mers consisting exclusively of A/T or G/C nucleotides for nucleosomes in coding regions (C) and intergenic regions (D) at the ring stage. Enrichment is expressed as the log 2 ratio of the frequency of a 5-mer inside nucleosomes and the genome-wide frequency of that 5-mer. E-F. Genome-wide frequency of each 5-mer plotted against the enrichment of each 5-mer in nucleosomes, shown for nucleosomes in coding regions (E) and intergenic regions (F). Nucleosomes inside coding regions show a strong binding preference for 5-mers with low genome-wide frequencies, while this association is absent for intergenic nucleosomes. AT-repeat 5-mers are indicated by a red circle. Pearson correlation coefficients are shown in the top right corner of each plot. G-H. Enrichment of AT-repeat 5-mers (ATATA and TATAT) in coding regions (G) and in the 500 nucleotides upstream of the translation start site (promoter region) (H) relative to their genome-wide frequency, for genes in each transcription cluster. Correlation coefficients were obtained using the Spearman’s rank test. I-J. Sequence composition in coding regions (I) and promoter regions (J) among genes with different expression levels. 5-mers were divided into five groups based on their genome-wide frequency in intergenic regions. For each transcription cluster, the z-normalized average log 2 ratio of 5-mer frequency in the gene or promoter versus all genes or intergenic regions, respectively, is plotted for all 5-mer frequency groups. Highly expressed genes show an increased prevalence of nucleosome-favorable 5-mers, while genes with low transcription levels show an increased prevalence of nucleosome-disfavorable 5-mers.