Figure 3.

DNMT1 is predominantly associated with oligonucleosomes in HCT116 cells, and decitabine treatment causes depletion but does not shift it to polynucleosomes. (A, B) HCT116 cells were treated with decitabine (1 µM) for 12 hours. Nuclei isolated from the washed cells were subjected to partial micrococcal nuclease digestion to yield nucleosomal fractions of different sizes. The nucleosomes were separated by sucrose density gradient centrifugation, and 18 fractions were collected (numbered 1-18 from the bottom to top of the gradient). Equal volume of protein from each fraction was analyzed by Western blot analysis. DNA purified from each fraction was separated on agarose gel and stained with ethidium bromide to visualize the distribution of mononucleosomes/polynucleosomes in the gradient.