The orientation bias of Chi sequences is a general tendency of G-rich oligomers

Reina Uno, Yoichi Nakayama, Kazuharu Arakawa, Masaru Tomita

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)


The Chi sequences are specific oligomers that stimulate DNA repair by homologous recombination, and are different sequences in each organism. Approximately 75% of the copies of the Chi sequence (5′-GCTGGTGG-3′) of Escherichia coli reside on the leading strand, and this orientation bias is often believed to be a consequence of the biological role of Chi sequences as the signal sequence of RecBCD pathway in DNA replication. However, our computer analysis found that many G-rich oligomers also show this asymmetric orientation pattern. The shift in the Chi orientation bias appears around the replication origin and terminus, but these locations are also coincident with the shift points in GC content or GC skew. We conducted the same analysis with the genome of Bacillus subtilis, and found that in addition to Chi, other G-rich oligomers show similar asymmetric orientation patterns, whose shift points were coincident with those of the GC skew. However, the genome of Haemophilus influenzae Rd, whose GC skew is not so pronounced, does not clearly show asymmetric orientation patterns of Chi or other G-rich oligomers. These results lead us to suggest that the uneven distribution of the Chi orientation between the two strands of the double helix is mostly due to the uneven distribution of G content (GC skew) and that the replication-related function of Chi sequences is not the primary factor responsible for the evolutionary pressure causing the orientation bias.

Original languageEnglish
Pages (from-to)207-215
Number of pages9
Issue number1-2
Publication statusPublished - 2000 Dec 23


  • Comparative genomics
  • Computational analysis
  • DNA replication
  • GC skew
  • Homologous recombination

ASJC Scopus subject areas

  • Genetics


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