G-Quadruplex enrichment analysis reveals their role as intronic regulatory elements in plants

Abstract

Introduction G-Quadruplexes (G4s) are a class of noncanonical and fourstranded DNA structures with roles revealed especially in chromatin maintenance and gene regulation (Burge et al., 2006). The first observations of G4s in biological samples were at telomeres where repeating G4s were demonstrated to prevent telomere elongation (Fletcher et al., 1998). It is not only telomeres where G4s were observed. Many nontelomeric G4s were found, surprisingly and more frequently, in genes associated with cancer and regulation (Eddy and Maizels, 2006; Huppert and Balasubramanian, 2007). The first indication of the role of G4s in gene regulation was observed in the c-myc promoter, where G-quadruplex disruptive mutations in the promoter lead to overexpression of c-myc (Grand et al., 2004). This was followed by several other promoter G4s (Cogoi and Xodo, 2006; Fernando et al., 2006; Sun et al., 2008), yet the regulatory effects of the G4s are not only limited to the promoter and associated with transcription initiation. They are also observed in UTRs and are associated with translation (