RT Journal
A1 Cayrou, Christelle
A1 Coulombe, Philippe
A1 Vigneron, Alice
A1 Stanojcic, Slavica
A1 Ganier, Olivier
A1 Peiffer, Isabelle
A1 Rivals, Eric
A1 Puy, Aurore
A1 Laurent-Chabalier, Sabine
A1 Desprat, Romain
A1 Méchali, Marcel
T1 Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
JF Genome Research 
JO Genome Research 
YR 2011 
FD September 01 
VO 21 
IS 9 
SP 1438 
OP 1449 
DO 10.1101/gr.121830.111 
UL http://genome.cshlp.org/content/21/9/1438.abstract 
AB In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS) purification and a genome-wide analysis in Drosophila and mouse cells. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, indicating that this epigenetic mark is not crucial for defining the activated origin. Initiation of DNA synthesis starts at the borders of CGI, resulting in a striking bimodal distribution of NS, suggestive of a dual initiation event. Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A overrepresentation at the 5′ and 3′ of Ori sites, respectively. Repeated GC-rich elements were detected, which are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions are late replicating. The genome-wide analysis was coupled with a DNA combing analysis to unravel the organization of Oris. The results indicate that Oris are in a large excess, but their activation does not occur at random. They are organized in groups of site-specific but flexible origins that define replicons, where a single origin is activated in each replicon. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation to environmental cues and cell fates.