The chromatin environment shapes DNA replication origin organization and defines origin classes

Abstract

To unveil the still-elusive nature of metazoan replication origins, we identified them genome-wide and at unprecedented high-resolution in mouse ES cells. This allowed initiation sites (IS) and initiation zones (IZ) to be differentiated. We then characterized their genetic signatures and organization and integrated these data with 43 chromatin marks and factors. Our results reveal that replication origins can be grouped into three main classes with distinct organization, chromatin environment, and sequence motifs. Class 1 contains relatively isolated, low-efficiency origins that are poor in epigenetic marks and are enriched in an asymmetric AC repeat at the initiation site. Late origins are mainly found in this class. Class 2 origins are particularly rich in enhancer elements. Class 3 origins are the most efficient and are associated with open chromatin and polycomb protein-enriched regions. The presence of Origin G-rich Repeated elements (OGRE) potentially forming G-quadruplexes (G4) was confirmed at most origins. These coincide with nucleosome-depleted regions located upstream of the initiation sites, which are associated with a labile nucleosome containing H3K64ac. These data demonstrate that specific chromatin landscapes and combinations of specific signatures regulate origin localization. They explain the frequently observed links between DNA replication and transcription. They also emphasize the plasticity of metazoan replication origins and suggest that in multicellular eukaryotes, the combination of distinct genetic features and chromatin configurations act in synergy to define and adapt the origin profile.

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

“…This result seems highly significant in light of the fact that in human cells, a simple model of DNA replication produced extremely accurate predictions of replication timing profiles when DNase I HS sites were used to construct a "probability landscape" for initiation (Gindin et al, 2014). Additionally, other studies have noted that DNase I or MNase HS sites are enriched in or near some classes of origins in humans and yeast (Audit et al, 2009;Rodriguez and Tsukiyama, 2013;Mukhopadhyay et al, 2014;Cayrou et al, 2015).…”

DNA replication origins—where do we begin?

“…The microarray-based studies laid the foundations for comprehensive genome-wide studies using next-generation sequencing (Martin et al 2011;Besnard et al 2012;Picard et al 2014;Cayrou et al 2015). These comprehensive surveys of origin activity were able to identify >80,000 origins that were activated in a variety of human ESC and mESC lines.…”

From structure to mechanism—understanding initiation of DNA replication

“…cerevisiae ORC recognizes specific DNA sequences within replication origins (Bell and Stillman 1992;Rao and Stillman 1995;Rowley et al 1995;Dueber et al 2007Dueber et al , 2011Gaudier et al 2007), while DNA structure and DNA-specific chromatin modifications appear more important for origin specification in metazoans (Remus et al 2004;Eaton et al 2011;Beck et al 2012;Kuo et al 2012;Cayrou et al 2015). Interestingly, Cdc6 also consists of an N-terminal AAA + domain and a C-terminal WHD, directly binds to ORC, and enhances the affinity and sequence specificity of budding yeast ORC (Speck et al 2005;Speck and Stillman 2007).…”

“…In contrast, D. melanogaster Orc4 and H. sapiens Orc4 are lacking the insertion α-helix and AT-hook domains. Intriguingly, metazoan replication origins share no common DNA sequence (Cayrou et al 2015;Hyrien 2015). However, H. sapiens Orc1 has affinity for G-quadruplex ssDNA (Hoshina et al 2013), shown to act as an origin-positioning motif (Valton et al 2014), while DNA topology has been shown to be an important determinant for Drosophila ORC-DNA interactions (Remus et al 2004).…”