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Originally published as Genetics Published Articles Ahead of Print on April 28, 2006.
Genetics, Vol. 173, 1259-1273, July 2006, Copyright © 2006
doi:10.1534/genetics.106.057364
Unusual DNA Structures Associated With Germline Genetic Activity in Caenorhabditis elegans
Andrew Fire1, Rosa Alcazar2 and Frederick Tan3
Departments of Pathology and Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218 and Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland 21218
1 Corresponding author: Departments of Pathology and Genetics, Stanford University School of Medicine, 300 Pasteur Dr., Room L235, Mail Stop M5324, Stanford, CA 94305-5324.
E-mail: afire{at}stanford.edu
We describe a surprising long-range periodicity that underlies a substantial fraction of C. elegans genomic sequence. Extended segments (up to several hundred nucleotides) of the C. elegans genome show a strong bias toward occurrence of AA/TT dinucleotides along one face of the helix while little or no such constraint is evident on the opposite helical face. Segments with this characteristic periodicity are highly overrepresented in intron sequences and are associated with a large fraction of genes with known germline expression in C. elegans. In addition to altering the path and flexibility of DNA in vitro, sequences of this character have been shown by others to constrain DNA::nucleosome interactions, potentially producing a structure that could resist the assembly of highly ordered (phased) nucleosome arrays that have been proposed as a precursor to heterochromatin. We propose a number of ways that the periodic occurrence of An/Tn clusters could reflect evolution and function of genes that express in the germ cell lineage of C. elegans.
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