Why are complementary DNA strands symmetric?
BACKGROUND
Over sufficiently long windows, complementary strands of DNA tend to have the same base composition. A few reports have indicated that this first-order parity rule extends at higher orders to oligonucleotide composition, at least in some organisms or taxa. However, the scientific literature falls short of providing a comprehensive study of reverse-complement symmetry at multiple orders and across the kingdom of life. It also lacks a characterization of this symmetry and a convincing explanation or clarification of its origin.


RESULTS
We develop methods to measure and characterize symmetry at multiple orders, and analyze a wide set of genomes, encompassing single- and double-stranded RNA and DNA viruses, bacteria, archae, mitochondria, and eukaryota. We quantify symmetry at orders 1 to 9 for contiguous sequences and pools of coding and non-coding upstream regions, compare the observed symmetry levels to those predicted by simple statistical models, and factor out the effect of lower-order distributions. We establish the universality and variability range of first-order strand symmetry, as well as of its higher-order extensions, and demonstrate the existence of genuine high-order symmetric constraints. We show that ubiquitous reverse-complement symmetry does not result from a single cause, such as point mutation or recombination, but rather emerges from the combined effects of a wide spectrum of mechanisms operating at multiple orders and length scales.
Baisnée
Pierre-François
PF
Department of Information and Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine 92697-3425, USA. baisnee@ics.uci.edu
Hampson
Steve
S
Baldi
Pierre
P
D001482:Base Composition; D001483:Base Sequence; D002875:Chromosomes; D003198:Computer Simulation; D018076:DNA, Complementary / Q000737:chemistry* / Q000235:genetics*; D030541:Databases, Genetic; D016678:Genome; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D015233:Models, Statistical; D003629:Modems; D008969:Molecular Sequence Data; D012313:RNA / Q000737:chemistry / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D017421:Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
D018076:DNA, Complementary; D012313:RNA