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Nucleic Acids Research, 1994, Vol. 22, No. 13 2479-2489
© 1994

MOLECULAR BIOLOGY

Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA

Drena L. Dobbs1,2,*, Wen-Ling Shaiu and Robert M. Benbow1,2,3

Department of Zoology and Genetics, Iowa State University Ames, IA 50011, USA 1Interdepartmental Genetics Major, Iowa State University Ames, IA 50011, USA 2Molecular, Cellular, and Developmental Biology Program Iowa State University, Ames, IA 50011, USA 3Nucleic Acid Research Facility, Iowa State University Ames, IA 50011, USA

*To whom correspondence should be addressed at: 2114 Molecular Biology Building, Iowa State University, Ames, IA 50011, USA

Received April 19, 1994. Revised May 23, 1994. Accepted May 23, 1994.

We have postulated that chromosomal replication origin regions in eukaryotes have in common clusters of certain modular sequence elements (Benbow, Zhao, and Larson, BioEssays 14, 661–670, 1992). In this study, computer analyses of DNA sequences from six origin regions showed that each contained one or more potential initiation regions consisting of a putative DUE (DNA unwinding element) aligned with clusters of SAR (scaffold associated region), and ARS (autonomously replicating sequence) consensus sequences, and pyrimidine tracts. The replication origins analyzed were from the following loci: Tetrahymena thermophila macronuclear rDNA gene, Chinese hamster ovary dihydrofolate reductase amplicon, human c-myc protooncogene, chicken histone H5 gene, Drosophila melanogaster chorion gene cluster on the third chromosome, and Chinese hamster ovary rhodopsin gene. The locations of putative initiation regions identified by the computer analyses were compared with published data obtained using diverse methods to map initiation sites. For at least four loci, the potential initiation regions identified by sequence analysis aligned with previously mapped initiation events. A consensus DNA sequence, WAWTTDDWWWDHWGWHMAWTT, was found within the potential initiation regions in every case. An additional 35 kb of combined flanking sequences from the six loci were also analyzed, but no additional copies of this consensus sequence were found.


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