A subset of nucleosomes demonstrate behaviors specific to H3 depletion.
(A) Schematic representation of the nucleosome classification method. Nucleosomes were classified based on changes in center positions and changes in read center counts between 0 hours and 3 hours (Materials and Methods). (B) Classification of nucleosomes. The number of nucleosomes in each classification that occur in only the wildtype strain 3 hours after the shift to Galactose (black); only the H3 shutoff strain (white); and those classified identically in both strains (gray) is shown. Only the H3 shutoff-specific nucleosomes (white) were used in subsequent analyses. The total number of nucleosomes that could be classified in each category are as follows: wildtype, 43,508; H3 shutoff, 38,955; classified in both, 28,717.