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

Osman DOLUCA

doi:10.3906/bot-1808-25

Abstract

G-Quadruplexes, a class of noncanonical but highly stable nucleic acid structures, have the potential to be part of the regulatory mechanism of cells. They can form in the genome where the double-stranded helix is unwound to facilitate formation of a G-quadruplex. The biological significance of these structures is yet to be understood entirely. This work presents a novel approach and investigates common characteristics in the distribution of G-quadruplexes relative to genes in plants through analysis of genomes and gene expressions. The results indicate that G-quadruplex distribution has gone through significant changes with the evolution of higher plants and, for the first time, that G-quadruplexes enriched at the beginning of introns may have a regulatory role during transcription.

Highlights

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 coexpression of O. sativa genes that contain a G4 at a particular hotspot is analyzed and clustered for the first time and the results provide the first indication of the role of G-quadruplexes in intron-mediated enhancement in plants
The G4 analysis showed that the most significant shifts or peaks in G4 intensities were observed in the vicinity of the first half of the features, transcription start site (TSS), AUG, and exon–intron boundary (EXINT), where most of the regulatory elements are located

Summary

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 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 limited to the promoter and associated with transcription initiation. They are observed in UTRs and are associated with translation (Huppert et al, 2008; Beaudoin and Perreault, 2013; Kwok et al, 2015)

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