The G4 genome

Abstract

Recent experiments provide fascinating examples of how G4 DNA and G4 RNA structures--aka quadruplexes--may contribute to normal biology and to genomic pathologies. Quadruplexes are transient and therefore difficult to identify directly in living cells, which initially caused skepticism regarding not only their biological relevance but even their existence. There is now compelling evidence for functions of some G4 motifs and the corresponding quadruplexes in essential processes, including initiation of DNA replication, telomere maintenance, regulated recombination in immune evasion and the immune response, control of gene expression, and genetic and epigenetic instability. Recognition and resolution of quadruplex structures is therefore an essential component of genome biology. We propose that G4 motifs and structures that participate in key processes compose the G4 genome, analogous to the transcriptome, proteome, or metabolome. This is a new view of the genome, which sees DNA as not only a simple alphabet but also a more complex geography. The challenge for the future is to systematically identify the G4 motifs that form quadruplexes in living cells and the features that confer on specific G4 motifs the ability to function as structural elements.

Figure 1. Structural variety of G4 DNA.

Top: A G4 motif consists of four runs of at least three guanines per run, separated by other bases (N). G4 motifs confer the ability to form a G4 DNA structure, also known as a “quadruplex” by analogy with the B-form DNA duplex. The essential unit of G4 DNA is the G-quartet, a planar array of guanines stabilized by Hoogsteen base pairing between the N7 group of one guanine and the extracyclic amino group of its neighbor. The guanines form a ring around a central channel that is occupied by a monovalent cation and associated water molecules (potassium is shown). G4 structures derive stability both from hydrogen bonding between guanines within G-quartets and from stacking of the planar, hydrophobic G-quartets. Middle: The length and sequence composition of the loops connecting planar arrays of G-quartets (left) and the parallel (near right) or antiparallel (far right) orientation of nucleic acid strands determine quadruplex topology. Bottom: There is considerable potential for structural polymorphism, as illustrated by the diagram of two possible conformations formed by the G4 motif G₃N₃G₃N₂G₄N₂G₅.

Figure 2. Structures form upon replication or transcription of regions bearing G4 motifs.

The figures illustrate how replication (left) or transcription (right) through G4 motifs ([G4]) may result in formation of structures. Replication is shown as arresting at a G4 motif in the leading DNA strand, as it does in Pif1-deficient yeast . Transcription is shown as resulting in formation of a G-loop, which contains a persistent RNA/DNA on the template strand and G4 DNA interspersed with single-stranded regions on the nontemplate strand .

Figure 3. G4 motif frequency in a generic human RefSeq gene.

Above, key elements of a generic gene are shown, including the TSS, 5′-UTR, 5′ exons and introns, and the 3′-UTR and poly(A) signal. Below, the graph shows the frequency of G4 motifs in each region (loop size 1–12 nt). G4 motif frequency was calculated by counting the number of times G4 motifs overlapped each position, and dividing by the number of regions surveyed, which varied for each window. G4 locations at the 5′-UTR–exon 1 boundary were calculated only for genes with a 5′-UTR that did not span multiple exons.