Genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests transcriptional importance of non-B DNA structures in Escherichia coli

Tuesday, October 09, 2012 — Poster Session I
1:00 p.m. – 3:00 p.m	Natcher Conference Center, Building 45	NLM	BIOINFO-6

* FARE Award Winner

Authors

• X Du
• D Wojtowicz
• A.A. Bowers
• C.J. Benham
• D.L. Levens
• T.M. Przytycka

Abstract

The canonical structure of DNA is right-handed double-stranded helix - B-DNA. However, DNA can also adopt alternative structures such as G-quadruplex, Z-DNA or cruciform. It has been long conjectured that non-B DNA can have broad regulatory roles, which has been supported by directed studies based on individual genes, as well as large scale, mostly indirect, analyses. In this study, we examined occurrences of non-B DNA motifs in the context of the operon structure in Escherichia coli. This setting provided a unique opportunity to compare the distribution of non-B DNA motifs in the regulatory regions of operons to the corresponding regions of genes that are internal to the operon. Indeed, we found there is an enrichment of non-B DNA motifs in the regulatory regions of operons and showed that this enrichment cannot be simply explained by the base composition of the E. coli genome. Additional analysis showed that the distribution of non-B DNA motifs in the intergenic region separating divergent or convergent operon pairs often differs. Finally, we observed enrichment of cruciform motifs in the termination region of genes with either Rho-independent or Rho-dependent terminators. These genome-wide analyses suggest that non-B DNA structures indeed play important regulatory roles in E. coli.

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