title: Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans.
abstract: 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.
authors.affiliation: Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA. afire@stanford.edu
authors.forename: Andrew
authors.initials: A
authors.lastname: Fire
authors.forename: Rosa
authors.initials: R
authors.lastname: Alcazar
authors.forename: Frederick
authors.initials: F
authors.lastname: Tan
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D019070:Cell Lineage; D018509:DNA, Helminth / Q000737:chemistry*; D019143:Evolution, Molecular; D044404:Genomic Islands; D005854:Germ Cells; D008969:Molecular Sequence Data; D016296:Mutagenesis; D016366:Open Reading Frames; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D018509:DNA, Helminth