G-quadruplex biology gained interest based on evidence supporting its widespread role as elements that can control or modulate gene regulation. This followed initial prediction based on computational analysis that found prevalence of quadruplex motifs in promoters of many bacterial and other organisms. In parallel, further evidence was found indicating the function of quadruplex motifs in replication, recombination and also DNA repair. In this review, we summarize recent findings that provide a new perspective by introducing quadruplex motifs in roles that support involvement during epigenetic events, in determining evolutionary selection and as possible determinants of quantitative expression traits (eQTL) across populations.