Preferential Localization of Human Origins of DNA Replication at the 5′-Ends of Expressed Genes and at Evolutionarily Conserved DNA Sequences (original) (raw)
Figure 1
Comparison of nascent DNA enrichment profiles obtained with MCF-7 nascent DNA fractions of increasing size.
(A) DNA from sucrose gradient fractions containing nascent DNA with a size range of, 0.7–1.5 kb (fraction 10–12); 1.5–3 Kb (fraction 18); and >3 kb (fraction 28) obtained from the same MCF-7 preparation were hybridized to the tiling array. As a control, sonicated total DNA in the size range of 0.7–1.5 kb was utilized as both test and reference DNA (self-self). After hybridization, the test/reference ratios (black dots) were processed to produce a smoothed line (red line). The peaks represent sites where enrichment of nascent DNA (origins) occurred along a 90 kb region of chromosome 17 (B) Comparison of origin profiles along two (13 kb and 43 kb respectively) selected regions on chr17 (indicated as bars in Figure 1A) obtained from either array data (red line) or from real-time PCR data (black line). (C) Peak spacing densities derived from nascent DNA enrichment profiles for the three DNA size range preparations hybridized to the array. Peaks were detected using a Savitzky-Golay filter with a 500 bp moving window over the genomic regions covered by the array. The number of peaks detected in each of the preparations is indicated in parentheses.