Project : Genetic and epigenetic nature of DNA replication origins

In contrast to bacterial or Saccharomyces cerevisiae, origins in multicellular organisms do not share a strict consensus genetic sequence. The availability of high-throughput methods allowed us to carry out genome-wide analysis of DNA replication origins from several mutlicellular organisms, including mouse embryonic stem cells (ES) cells (Cayrou et al, 2011; Cayrou et al, 2012 ; Cayrou et al, 2015), Drosophila cells (Cayrou et al, 2011), C. elegans embryos (Rodriguez et al, 2017), and human cells (Akerman et al, 2020).
However, the high resolution of the SNS-Seq origin mapping method led us to identify one common, repeated consensus element in all tested organisms,  that we called OGRE, for Origin G-rich Repeated Element (Cayrou et al, 2012, Cayrou et al, 2015 and Figure 1). This motif is unexpectedly G-rich, in contrast to the AT richness of bacterial and yeast DNA replication origins. We also showed that OGREs can form G quadruplexes (G4s), and that DNA synthesis initiates at a short distance downstream of these elements (Cayrou et al, 2011; Cayrou et al, 2012; Cayrou et al, 2015; Akerman et a, 2020).

Figure 1: OGRE/G4 elements and initiation of DNA replication. OGRE/G4 elements are upstream of the initiation site of DNA synthesis (From Cayrou et al, 2011, 2012, 2015).

We also identified three distinct classes of DNA replication origins, characterized by specific epigenetic marks (Cayrou et al, 2015). These results highlight the plasticity of DNA replication origins according to their chromosomal contexts. Our DNA combing experiments also showed that replication origins are flexible, because only a minor fraction of all potential DNA replication origins is activated at each cell cycle in a given cell, in an apparent stochastic manner. The excess of potential DNA replication origins appears to be an important genome safeguard mechanism to ensure that all sequences are duplicated during the cell cycle. It might also permit to choose the DNA replication origins to be activated according to the pattern of gene expression in a given cell. Our goal is now to understand how these elements play a role in the 3D structure of the genome.