Figure 1.
Nucleosome ladder and compositional distribution of low molecular weight (LMW) DNA fragments.
(A) Chicken liver was cut into small pieces and immediately put in sterile tubes for 1 hr at 37°C (AU). Chicken liver nuclei were digested with 300 U of MNase for 30 sec. at 37°C (MN). DNA was purified from both preparations and run on 2% agarose gel producing a “nucleosome ladder”. The marker Smart Ladder Eurogentec is also shown (M). Compositional distribution of chicken DNA and of low molecular weight (LMW) DNA fragments after autolysis (B) or MNase digestion (C). The GC level of the LMW DNA fragments (average length ∼200 bp, red line) was superimposed on the GC profile of the chicken genome (blue line), as assessed at a window size of 200 bp. The frequency of the segments (×10−6) was indicated on the left and right ordinates for the chicken genome and the LMW DNA fragments respectively.
Figure 2.
Density of apoptotic and MNase LMW cloned DNA fragments in isochore families.
The bottom panel shows the amount of DNA in each isochore family of the chicken genome.
Figure 3.
Mapping of apoptotic and MNase cuts on chicken chromosome 1.
The GC level and the gene density in the isochores are shown for the telomeric 60 Mb of the p arm of chicken chromosome 3. The arrows indicate the cuts (in red for the autolysis and in black for MNase digestion). The down- and up- pointed arrows ↓ ↑ indicate cuts in genes or in sequences within 50 kb (asterisks) or 100 kb from genes. Cut mapping on all other chromosomes is reported in Figure S1.
Figure 4.
Map distances (as % of total distances) among clones from autolysis and MNase.
Histogram are presented in Mb bins (top yellow segments refer to redundant clones; inserts refer to distances lower than 500 kb).
Table 1.
Sequences cleaved by autolysis and MNase.
Table 2.
Number of clones, redundancies, sites, and minimal distances between the location of the clones derived from apoptotic or MNase degradation and between the two kinds of cuts.
Figure 5.
Scheme of autolytic and MNase cuts within 100 kb.
Maps of MNase and autolytic cuts (black and red arrows, respectively) and of genes (colored stretches) located at (and between) cuts. See Table S3 online for the origin and description of the genes presented in the Figure.