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Open Access Highly Accessed Research

Unusual DNA packaging characteristics in endoreduplicated Caenorhabditis elegans oocytes defined by in vivo accessibility to an endogenous nuclease activity

Sam Guoping Gu4*, Barbara Goszczynski3, James D McGhee3 and Andrew Z Fire12*

Author Affiliations

1 Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive-L302, Stanford, CA 94305, USA

2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA

3 Department of Biochemistry and Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary AB T2N 4 N1, Canada

4 Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA

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Epigenetics & Chromatin 2013, 6:37  doi:10.1186/1756-8935-6-37

Published: 1 November 2013

Abstract

Background

Germ cells in animals are highly specialized to preserve the genome. A distinct set of chromatin structures must be properly established in germ cells to maintain cell fate and genome integrity. We describe DNA-surface interactions in activated Caenorhabditis elegans oocytes that are revealed through the activity of an endogenous nuclease ('endocleavage’).

Results

Our analysis began with an unexpected observation that a majority (>50%) of DNA from ovulated but unfertilized C. elegans oocytes can be recovered in fragments of approximately 500 base pairs or shorter, cleaved at regular intervals (10 to 11 nt) along the DNA helix. In some areas of the genome, DNA cleavage patterns in these 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 approximately 10 bp 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 endocleavage 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.

Conclusion

The present analysis provides evidence for an unusual structure in C. elegans oocytes in which genomic DNA and associated protein structures are coherently linked.