Figure 1.
The GC content in 147 base pair windows is strongly correlated to nucleosome occupancy.
Density plot comparison between the normalized centered GC content in 147 base pair windows (x axis) and (A) the in vitro reconstituted, (B) the in vivo (YPD) and (C) the predicted nucleosome map (y axis). The color of each point represents the density of base pairs mapping to it, where the density-color relationship is shown at the right of each plot. The Pearson correlation coefficients r between the data sets is indicated.
Figure 2.
Exemplary profiles in a region of chromosome I.
Shown is an exemplary region (40,000 to 50,000 base pairs) of chromosome I of S. cerevisiae. The blue boxes mark the open reading frames of annotated genes, where the direction of the arrowheads correspond to the direction of transcription. The profiles of the in vivo (blue), in vitro (green) and the MNase digestion of naked DNA (gray) are shown underneath. The y axes of these profiles correspond to the nucleosome occupancy/coverage per base pair normalized by dividing by the genome wide average. The dashed line at 1.0 therefore corresponds therefore to the genome wide average. The last track shows the GC-content (black) in percent in 147 base pair windows centered around the central base pair. The arrow indicates the presumable +1 nucleosome of YAL053W and the gray box marks the nucleosome depleted region immediately upstream (see Text for details).
Figure 3.
MNase digestion leads to systematic measurement bias.
(A–C) Density plot comparison between the normalized coverage per base pair in the MNase generated map on naked DNA (x axis) and (A) the in vitro reconstituted, (B) the in vivo (YPD) and (C) the predicted nucleosome map (y axis). The color of each point represents the density of base pairs mapping to it, where the density-color relationship is shown at the right of each plot. The Pearson correlation coefficients r between the data sets are indicated. (D) The GC-content profile in percent (3 base pair moving average) around the start coordinate of the reads. The gray filled curve corresponds to the profile obtained by digesting naked DNA with MNase and the blue and green curve represent the profile for the in vitro and in vivo (YPD) data, respectively. The dashed horizontal line indicates the average GC content in the yeast genome (38.3%) and the box indicates the selected fragment (0–149 base pairs).
Figure 4.
Comparison of the average genome wide relative coverage of sequence of length 5.
(A) the MNase generated map on naked DNA (x axis) and the in vitro reconstituted nucleosome map (y axis); (B) the MNase generated map on naked DNA (x axis) and the in vivo (YPD) nucleosome map (y axis); (C) the in vivo (YPD) nucleosome map (x axis) and the in vitro nucleosome map (y axis). The Pearson correlation coefficients r between the data sets are indicated.
Figure 5.
Nucleosome positioning in the Gal1-10 Locus.
Shown is the Gal1-10 locus on chromosome II (277,554 to 279500). The blue boxes mark the open reading frames of annotated genes, where the direction of the arrowheads correspond to the direction of transcription. The transcription factor binding sites are from Harbison et al. (2004) [45]. The DNAse I tag numbers are from Hesselberth et al. (2009) [42], shown on the y axis is the number of tags for each position. Nucleosome positions determined by Li and Smerdon (2002) are denoted as black boxes [40]. The profiles of the in vivo (blue), in vitro (green) and the MNase digestion of naked DNA (gray) are shown underneath. The y axes of these profiles correspond to the nucleosome occupancy/coverage per base pair normalized by dividing by the genome wide average. The dashed line at 1.0 therefore corresponds therefore to the genome wide average. The last track shows the GC-content (black) in percent in 147 base pair windows centered around the central base pair. The gray box denotes the UAS of Gal1 and Gal10.