Figure 5

Rotational positioning of the activated oocyte chromatin in regions that are enriched for the periodic A(n)/T(n) clusters (PATC). (a) An example of examining the endo-cleavage events for different rotational phasing of the DNA double helix. A DNA segment of strong PATC character was selected from the intronic sequence of gene F54C4.1. Integer numbers from 0 to 9 below each line of sequences are used to indicate the PATC phasing number (that is, the positions relative to the A(n)/T(n) face, which is designated as 0). In a second line, the numbers of endo-cleavage events are indicated. The accessibility for each of the ten phase bins is measured by summing the endo-cleavage events occurring at the same face. The bar graph plots the endo-cleavage frequency as a function of the PATC phasing number. (b) For genome-wide analyses, the total endo-cleavage sites for each of the ten phase bins were separated into 256 classes according to the cleavage site sequence (NN|NN). The comparison of DNA accessibility among the ten phase bins was then performed by using cleavage sites of the same sequence, generating a total of 256 comparisons. For each of the 256 tetramer sequences, cleavage frequency (normalized by the frequency of the corresponding tetramer at the cleavage sites) is plotted as a function of the PATC phasing number for activated fer-1(b232) oocytes. (c) Same analysis performed on MNase-digested naked DNA and nucleosome cores.