Journal of Molecular Evolution

, Volume 57, Issue 3, pp 325–334

Strand Compositional Asymmetries of Nuclear DNA in Eukaryotes

Article

DOI: 10.1007/s00239-003-2483-9

Cite this article as:
Niu, D.K., Lin, K. & Zhang, DY. J Mol Evol (2003) 57: 325. doi:10.1007/s00239-003-2483-9

Abstract

Both DNA replication and transcription are structurally asymmetric processes. An asymmetric nucleotide substitution pattern has been observed between the leading and the lagging strand, and between the coding and the noncoding strand, in eubacterial, viral, and organelle genomes. Similar studies in eukaryotes have been rare, because the origins of replication in nuclear genomes are mostly unknown and the replicons are much shorter than those of prokaryotes. To circumvent these predicaments, all possible pairs of neighboring genes that are located on different strands of nuclear DNA were selected from the complete genomes of Saccharomycescerevisiae, Schizosaccharomycespombe, Plasmodiumfalciparum, Encephalitozooncuniculi, Arabidopsisthaliana, Caenorhabditiselegans, Drosophilamelanogaster, Anophelesgambiae, Musmusculus, and Homosapiens. For such a pair of genes, one is likely coded from the leading strand and the other from the lagging strand. By examining the introns and the fourfold degenerate sites of codons in the genes of each pair, we found that the relative frequencies of T vs. A and of G vs. C are significantly skewed in most eukaryotes studied. In a gene pair, the potential effects of replication- and transcription-associated mutation bias on strand asymmetry are in the same direction for one gene where leading strand synthesis shares the same template with transcription, while they tend to be canceled out in the other gene. Our study demonstrates that DNA replication-associated and transcription-associated mutation bias and/or selective codon usage bias may affect the strand nucleotide composition asymmetrically in eukaryotic genomes.

Keywords

DNA replication Eukaryote Mutational bias Single strand Strand asymmetry Transcription 

Copyright information

© Springer-Verlag New York Inc. 2003

Authors and Affiliations

  1. 1.MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life Sciences, Beijing Normal University, Beijing 100875China

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