Competitive superhelical transitions involving cruciform extrusion

D Zhabinskaya,C J Benham

doi:10.1093/nar/gkt733

Abstract

A DNA molecule under negative superhelical stress becomes susceptible to transitions to alternate structures. The accessible alternate conformations depend on base sequence and compete for occupancy. We have developed a method to calculate equilibrium distributions among the states available to such systems, as well as their average thermodynamic properties. Here we extend this approach to include superhelical cruciform extrusion at both perfect and imperfect inverted repeat (IR) sequences. We find that short IRs do not extrude cruciforms, even in the absence of competition. But as the length of an IR increases, its extrusion can come to dominate both strand separation and B-Z transitions. Although many IRs are present in human genomic DNA, we find that extrusion-susceptible ones occur infrequently. Moreover, their avoidance of transcription start sites in eukaryotes suggests that cruciform formation is rarely involved in mechanisms of gene regulation. We examine a set of clinically important chromosomal translocation breakpoints that occur at long IRs, whose rearrangement has been proposed to be driven by cruciform extrusion. Our results show that the susceptibilities of these IRs to cruciform formation correspond closely with their observed translocation frequencies.

Highlights

DNA in vivo is found mainly as a right-handed B-form helix, in principle it can assume any of several other conformations
We examine the superhelical competition between denaturation, Z-DNA and cruciform formation in a simplified yet illustrative situation
We have developed and applied computational methods to analyze cruciform extrusion in negatively superhelical DNA molecules having any base sequence, both in isolation and in competition with strand separation and B-Z transitions

Summary

Introduction

DNA in vivo is found mainly as a right-handed B-form helix, in principle it can assume any of several other conformations Some, such as the A-form and strand separated DNA, can occur in any base sequence, the latter is favored in locally A+T-rich regions. Substantial levels of negative superhelicity are imposed on DNA by gyrase enzymes in prokaryotes and by transcriptional activity in all organisms [1] In eukaryotes this transcriptional superhelicity is transient, it is known to be substantial, generating a superhelix density of s = À0.07, to travel over kilobase distances and to persist long enough to drive DNA structural transitions within this region [2]. The latter investigation found eukaryotic chromosomes to be partitioned into large-scale topological domains, with negative superhelicity occurring in domains where significant transcriptional activity was taking place

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