Figure 3

CentC alignments and micrococcal nuclease (MNase) sequence preference. (A) The number of alignment edges at each position on CentC from CENH3-ChIP reads. Due to the short and repetitive character of Cent, just the alignment edges are depicted rather than the entire alignments. An apparent preferred position is defined by right edges positioned over the bracketed section (but see B). Alignments to CentC were split into two categories, forward and reverse orientation; then the 5'-most position of the forward alignments were combined with the 3'-most position of the reverse alignments to count the total number of left edge positions along the length of CentC. Likewise, the 5'-most position of the reverse alignments and 3'-most position of the forward alignments were combined to count the total number of right edge positions. Since this analysis uses only information from alignment edges, the alignments were first filtered so as to include only the ones with approximate nucleosome lengths (145 to 175 bp). (B) Sequence preference in MNase digestion of CentC. DNA fragments produced by MNase digest of naked DNA or chromatin were captured by ligation to adapters then amplified with primers that selected for CentC-adapter junctions (corresponding to the right edges shown in A). The bar chart indicates the number of cloned fragments (per 100) whose right edges were within 3 bp of the enriched site found in the CENH3-ChIP 454 dataset (the bracketed section in A, centred on the last base in GGGTGTCGGGGTG). Errors bars are standard errors of the means, calculated based on the sample sizes (74 sequences for 'Naked DNA No.1', 37 for 'Naked DNA No.2', 46 for 'Naked DNA No.3', 46 for 'Naked DNA No.4', 71 for 'Chromatin No.1', 41 for 'Chromatin No.2' and 47 for 'Chromatin No.3'.