G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae

John A Capra,Mona Singh,Katrin Paeschke,Virginia A Zakian,Gary D Stormo

doi:10.1371/journal.pcbi.1000861

Abstract

G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs) across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs). Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.

Highlights

DNA primarily exists as a double helix
All results are based on the set of motifs with loops of 25 nt or less. (The genome locations of these G4 DNA motifs are given in Dataset S1.) This threshold was selected to include the longest previously reported loop in a G4 DNA structure (22 nt) [26]
Regions containing more than four G-tracts separated by less than a given loop length threshold were counted as a single motif. (See Methods for a comparison of our motif definition with previous approaches.) In this paper, ‘‘G4 DNA motif’’ refers to DNA sites that match this sequence pattern, and ‘‘G4 DNA structure’’ refers to the G-quadruplex DNA secondary structure potentially formed by sequences containing the G4 DNA motif

Summary

Introduction

DNA can adopt other structural conformations that have the potential to play critical roles in a range of biological processes. One such structure is G-quadruplex DNA (G4 DNA structure), which was discovered in the late 1980s when biochemical experiments demonstrated that oligodeoxynucleotides that contain four separated runs of two, three, or four guanines (G-tracts) can spontaneously form four-stranded structures [1,2] (Fig. 1A). G4 DNA structures consist of stacked planar G-quartets that are held together by Hoogsteen hydrogen bonding between four guanines from each of the G-tracts (Fig. 1B). G4 DNA structures can be formed from runs of two guanines, but they are less stable than those with longer runs

Methods

Results

Discussion

Conclusion