Journal Article

Methods for Comparing Sources of Strand Compositional Asymmetry in Microbial Chromosomes

Robert H. Baran, Hanseok Ko and Robert W. Jernigan

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 10, issue 3, pages 85-95
Published in print January 2003 | ISSN: 1340-2838
Published online January 2003 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/10.3.85

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Significant compositional biases in bacterial chromosomes have been explained by replication- and transcription-coupled repair mechanisms, the latter causing GC skew to indicate the direction of replication when gene polarity is correspondingly entrained. Correlations between indicators of replication direction, skew, and transcription polarity are computed for the complete nucleotide sequences of 20 microbialc hromosomes and interpreted through statistical tests. A second quantitative method, previously applied to the first complete draft of the Escherichia coli K12 genome, characterizes the sequences by average skew and net skew due to replication. These methods generally agree in finding the coexistence of replication- and translation-coupled effects and in identifying atypical sequences in which one influence is clearly dominant. The replication-dominated class is exemplified by two chlamydial sequences and the transcription-dominated class by three archaea. The preference for leading-strand transcription in two mycoplasmas is stronger than the skew implies. These concordant methods provide an objective framework for comparing sources of strand compositionalasymmetry and interpreting skew diagrams.

Keywords: DNA replication and repair; transcription; base composition; GC skew; comparative genomics

Journal Article.  0 words. 

Subjects: Genetics and Genomics

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