Fig. 3

Comparison between chemical map-based and MNase-seq-based models on selected in vivo regions. A, B Chemical map-based and MNase-seq-based HBA scores (A) and A/T nucleotide frequency (B) along the sequences containing budding yeast − 1 and + 1 nucleosomes for protein-coding genes. Gray vertical lines indicate the dyad positions of respective nucleosomes. Nucleosomes of which the dyad base is located at 0 bp are shown as ovals above the plots. Asterisks indicate positions with relatively high HBA scores. NDR: nucleosome-depleted region. c Prediction results for the budding yeast TRP1ARS1 mini-chromosome. Schematic representation of in vivo nucleosome positioning is shown above the plots. Nucleosomes labeled I through VII are indicated as ovals. Note that this sequence is circularized in vivo by being linked at the EcoRI sites. The top two panels show the prediction results output by nuCpos, whereas the next two panels show NuPoP results. The upper panel in each set shows predicted occupancy of the nucleosome (Occup., gray polygons) and probabilities of the tested 147-bp sequences for being in the nucleosome state (P-dyad, blue vertical lines). The lower panels show HBA values for the tested 147-bp sequences calculated using the indicated models. The very bottom panel shows the A/T-frequencies for the tested 147-bp sequences. Horizontal lines at the bottom of each plot indicate a unit of the circular TRP1ARS1 mini-chromosome (colored in gray, nucleotide positions 0–1464), the coding region of TRP1 (red, 115–879), and the B3 (black, 763–788), B2 (purple, 810–820), B1 (green, 847–859), and ACS (blue, 869–879) elements of ARS1. Inverted triangles indicate the histone H4 S47C-dependent cleavage centers determined by indirect end-labeling; orange for mini-chromosome and light blue for genomic experiments [24]