Genomic Features: Content Sensors, Nucleotide Skew Plot, Strand Asymmetry, and DNA Methylation

  • Xuhua Xia


This chapter introduces tools to characterize genomic features and illustrates how a phylogenetic perspective can fundamentally alter one’s conclusion on genomic evolution. The chapter starts by explaining content sensors (e.g., nucleotide, dinucleotide, triplet frequencies, etc.) in contrast to signal sensors (e.g., 5’ and 3’ splice sites, branchpoint sites, SD sequences, anti-SD sequences, Kozak consensus in mammalian mRNAs, sense and stop codons, etc.). Frequently used indices for characterizing genomic content sensors include various word skews, with the simplest being GC skew often used to identify the origin of DNA replication in prokayrotes. Single-origin replication in most bacterial genomes results in strong mutation bias between leading and lagging strands which can be graphically revealed by various skew plots. Confounding these strand biases is the genomic modification by DNA methylation which can have profound effect on genome evolution. Association between CpG deficiency and CpG-specific DNA methylation was challenged previously with two mycoplasma genomes but is restored by a phylogeny-based reanalysis and re-interpretation of the genomic data.


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Authors and Affiliations

  • Xuhua Xia
    • 1
  1. 1.University of Ottawa CAREG and Biology DepartmentOttawaCanada

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