Computational Analysis of the Strand Bias of the Chi Sequences and Other Oligonucleotides in Bacterial Genomes

Abstract

A Chi sequence (5’-GCTGGTGG-3’) in Escherichia coli is an 8bp sequence element that promotes recombination by attenuating the activity of RecBCD enzyme. Upon recognition of the Chi sequence, the 3’ to 5’ exonuclease activity of RecBCD is suppressed and weaker 5’ to 3’ exonuclease function is activated. The helicase function of RecBCD remains unchanged. The Chi sequence is overrepresented in the genome, and mostly exists in the ORF [3]. 75% of the Chi sequences have a strand bias towards the direction of replication, and this strand bias is believed to have derived from the role of RecBCD in the reconstruction of replication fork [2]. However, the analysis of the strand bias of all oligomers compared with their G contents revealed that the strand bias of the Chi sequence towards the direction of replication is a general tendency of G rich oligomers [4]. Bell et al. observed that the orientation of the Chi sequence correlate better with transcription rather than with replication [1]. In this work, we analyze the strand bias of all oligomers towards the direction of transcription, in the genomes of E. coli, Bacillus subtilis, Haemophilus influenzae Rd.