Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates

Replication of vertebrate genomes is tightly regulated to ensure accurate duplication, but our understanding of the interplay between genetic and epigenetic factors in this regulation remains incomplete. Here, we investigated the involvement of three elements enriched at gene promoters and replication origins: guanine-rich motifs potentially forming G-quadruplexes (pG4s), nucleosome-free regions (NFRs), and the histone variant H2A.Z, in the firing of origins of replication in vertebrates. We show that two pG4s on the same DNA strand (dimeric pG4s) are sufficient to induce the assembly of an efficient minimal replication origin without inducing transcription in avian DT40 cells. Dimeric pG4s in replication origins are associated with formation of an NFR next to precisely-positioned nucleosomes enriched in H2A.Z on this minimal origin and genome-wide. Thus, our data suggest that dimeric pG4s are important for the organization and duplication of vertebrate genomes. It supports the hypothesis that a nucleosome close to an NFR is a shared signal for the formation of replication origins in eukaryotes. A program regulating replication origins ensures the exact duplication of vertebrate genomes. The authors identify a combination of guanine-rich motifs, known to form secondary DNA structures, which are sufficient to assemble efficient replication origins.

Automated summary

In this study, the involvement of three elements (guanine-rich motifs potentially forming G-quadruplexes, nucleosome-free regions, and the histone variant H2A.Z) in the firing of replication origins in vertebrates were investigated. It was found that two guanine-rich motifs on the same DNA strand were sufficient to assemble a functional replication origin without inducing transcription. The guanine-rich motifs were associated with the formation of nucleosome-free regions and enrichment of H2A.Z. These findings suggest the importance of guanine-rich motifs in the organization and duplication of vertebrate genomes.