Nucleic Acids Research, 2006, Vol. 34, No. 7 1977 Figure 1. Predicted and experimentally determined nucleosome arrangements for two loci. (A) FTs of the curves of the oscillations of period-10 VWG with nucleotide number for 100 kb windows. Probe 9–403 (left) was from the center of a locus on chromosome 9 that does not possess a predominant in-phase period-10 VWG oscillation, thus predicting that nucleosome arrays in this locus should have the properties of the bulk chromatin. Probe 4–419 (right) was from the center of a locus on chromosome 4 that exhibits a predominant in-phase period-10 VWG oscillation at a period of 337 bp (arrow), thus predicting a nucleosome array with a very short nucleosome repeat value of 337 bp/2 ¼ 169 bp. The Fourier curve (black points and spline curve) was represented by five Gaussian peaks (blue curves) that summed (orange circles) to fit the computed Fourier points in the physiological dinucleosome region. (B) Southern blots of agarose gel electrophoresis of the DNA fragments obtained from MNase digests of nuclei. Portions of the same digests were probed with probe 9–403 (left) or probe 4–419 (right), and the resultant nucleosome ladders were compared. Lanes 1 were from a 1.5 min digest and lanes 2 were from a 2 min digest. Lanes D were from a HindIII + PstI digestion of purified mouse liver genomic DNA to assess the specificity of the probes, lanes M1 were labeled 100 bp ladders (sizes of selected fragments are indicated on the right) for nucleosome oligomer sizing, and lanes M2 were labeled size markers (see Materials and Methods) for restriction fragment sizing. The nucleosome 2, 4 and 6mers detected by each probe are identified. (C) Analysis of the nucleosome repeat length from the ladders of the 2 min digest detected with each probe. Plots of nucleosome oligomer size (Base pairs) versus nucleosome oligomer number are shown. Probe 9–403, squares; probe 4–419, circles. The equations of the best straight line fits and the R2 values are shown. The nucleosome repeat lengths are the slopes of the lines. window, and the DNA from a single MNase digest of mouse liver nuclei (with 1.5 or 2 min time points) was examined separately using each probe (Figure 1B). The nucleosome ladder (lane 1) detected by the 9–403 probe closely resembled that of bulk chromatin, whereas a portion of the same sample detected by the 4–419 probe revealed a ladder with a consid- erably shorter repeat. For example, it can be seen directly from the autoradiograms that for the 9–403 probe the nucleosome 4 and 5mer fragments run close to the 800 and 1000 bp fragments, respectively, of the adjacent 100 bp ladder marker, whereas for the 4–419 probe the nucleosome 4 and 5mer fragments run close to the 700 and 900 bp marker fragments, respectively, of the adjacent 100 bp ladder. A detailed analysis of the ladders is presented in Figure 1C. For each ladder the plot of the nucleosome oligomer size (bp) against nucleosome oligomer number is a straight line with a slightly negative y-intercept and a standard deviation of the ﬁt value of 11–12 bp, indicating that the nucleosome oligomers are