Unusual DNA packaging characteristics in endo-reduplicated C. elegans oocytes defined by in vivo accessibility to an endogenous nuclease activity
We describe DNA-surface interactions in activated C. elegans oocytes that are revealed through the activity of an endogenous nuclease. Our analysis began with an unexpected observation that a majority (>50%) of DNA from C. elegans fer-1 oocytes can be recovered in fragments of  ~500 base pairs or shorter, cleaved at regular intervals (10-11nt) along the DNA helix. In some areas of the genome, cleavage patterns in the endoreduplicated oocytes appear consistent from cell-to-cell, indicating coherent rotational positioning of the DNA in chromatin. Particularly striking in this analysis are arrays of sensitive sites with a periodicity of ~10bp that persist for several hundred base pairs of genomic DNA, longer than a single nucleosome core.  Genomic regions with a strong bias toward a 10-nt periodic occurrence of A(n)/T(n) (so-called PATC regions) appear to exhibit a high degree of rotational constraint in endo-cleavage phasing, with a strong tendency for the periodic A(n)/T(n) sites to remain on the face of the helix protected from nuclease digestion. Overall, the present analysis provides evidence for an unusual structure in C. elegans oocytes in which genomic DNA and associated protein structures are coherently linked. Overall design: Examine endocleavage pattern in C. elegans fer-1 oocyte chromatin