1978 Nucleic Acids Research, 2006, Vol. 34, No. 7 Table 1. Computational predictions of nucleosome repeats base upon the DNA sequence and the results of the experimental tests of these predictions in mouse liver nuclei Locus number Chromosome Nucleosome repeat number-probe Theoretical Experimental size (bp) predictiona (bp) valueb (±5 bp) Experiment fit param. Fourier signal characteristics (Gaussian) Y-intercept SD of fit (bp) Peak SD (bp) Peak height Ratioc Window (kb) Predicted (VWG count) ranged (kb) 1 2 3 4 5 6 7 8 9 10 Madaf 4–419 7–500 3–413 7–474 10–336 2–375 2–450f 12–573 15–407 3–552 2–820 3–342 19–395 1–678 9–403 18–735 Et brf 337/2 ¼ (169)e 172 348/2 ¼ 171 172 347/2 ¼ 174 174 348/2 ¼ 174 178 358/2 ¼ 179 176 358/2 ¼ 179 180 357/2 ¼ 179 183 359/2 ¼ 180 179 360/2 ¼ 180 180 360/2 ¼ 180 181 370/2 ¼ 185 183 381/2 ¼ 191 190 4b2ul0k/g2 ¼ (210) 187 191 bulkg 192 bulkh 194 bulk 194 0.6 1.4 0.7 4.6 5.4 0.6 1.3 14 23 2.1 3.8 17 11 12 7.8 42 33 11 5.8 8.5 7.2 6.5 13 12 2.8 11 4.9 9.2 9.2 5.7 9.2 12 8.1 10 9.0 8.0 7.0 15 9.0 17 16 7.0 14 7.5 7.5 10.5 14 1174 773 1653 918 975 811 960 1368 788 931 1011 855 1052 2.2 2.1 4.5 6.6 3.1 9.3 7.0 3.4 5.0 3.7 2.2 3.8 2.6 100 100 120 100 100 90 100 100 100 90 110 120 100 90–110 90–110 40–500 90–200 70–120 80–100 90–170 70–130 90–110 70–110 70–130 100–130 90–110 aDinucleosome period mean value (of predominant Gaussian)/2 ¼ predicted nucleosome repeat. bAll probes exactly centered on the computation window of best ratio. cRatio of the signal peak area to the next largest peak area in the physiological region. dRange over which peak area of interest is at least two times greater than the next highest Gaussian in the physiological range. eParentheses denote extreme values that might not be physiological for mouse liver chromatin. fSee reference (17). gNo signal. hnon-specific probe. close to being multiples of a unit repeat, and therefore that the arrays are periodic. However, the repeat values differ substantially. The nucleosome repeat for the 9–403 region is 192 ± 5 bp, whereas the repeat for the 4–419 region is 172 ± 5 bp, 20 bp shorter. These repeat values are consistent with our computational predictions. The 172 ± 5 bp nucleosome repeat length is, to our knowl- edge, the shortest repeat ever observed in mouse liver chro- matin. Thus, nucleosome arrays possessing very short repeats exist in mouse liver nuclei. Moreover, our results suggest that it may be possible to predict these regions computationally from the genomic DNA sequence. Testing our ability to predict regions of the mouse genome that have short nucleosome repeats Table 1 shows the results of nine additional experiments simi- lar to the one reported in Figure 1 (probe 4–419) which test the validity of our computational predictions of short repeats. The table entries are arranged in order of increasing predicted repeats. In every case the experiment conﬁrmed the compu- tational prediction for the short nucleosome repeat value within the experimental uncertainty of ±5 bp. The character- istics of each signal are also listed, along with the predicted range of the signal. The range (in kb) over which the signal was strong according to the criteria stated in the Materials and Methods was tested by varying the Fourier window. It was usually fairly narrow and roughly centered on 100 kb. An example is shown in Figure 2 where the window size was varied from 7 to 120 kb for probe 4–419. All of the windows were centered on the 419 bp probe. It can be seen that for the 7 and 15 kb windows, the Amplitude at the Period value of Figure 2. Effect of varying the window size on the FT of the period-10 VWG oscillations for locus 1. All windows were centered on the midpoint of probe 4–419. The superimposed curves for windows ranging from 7 to 120 kb can be distinguished from each other by their colors. 337 bp (¼ 2 · 169 bp) is barely above the noise level. For a window of 30 kb, a small peak appears at the Period value of 337 bp, and this peak is only slightly larger than the next largest peak just below 400 bp. The Amplitude at the Period value of 337 bp becomes progressively larger as the window size increases to 60, 75 and 100 kb, respectively. The predominant peak (at 337 bp) meets our criterion of a strong signal by having at least twice the area of any other (Gaussian)