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doi:10.1534/genetics.106.057364
A more recent version of this article appeared on July 1, 2006.
REGULAR RESEARCH PAPERS |
Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans
Andrew Fire 1*, Rosa Alcazar 2 and Frederick Tan 3
1 Stanford University School of Medicine
2 Stanford University/Johns Hopkins
3 Johns Hopkins University
* To whom correspondence should be addressed. E-mail: afire{at}stanford.edu.
Submitted on February 17, 2006
Revised on April 10, 2006
Accepted on 21 April 2006
We describe a surprising long-range periodicity which 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 which 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 which express in the germ cell lineage of C. elegans.
Key Words: C. elegans, Genome Structure, Periodicity
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