Marie-Noelle Prioleau, Institut Jacques Monod - Université Paris Diderot

Contact : Franck Picard / Olivier Gandrillon

DNA replication is a universal process initiated at specific loci called replication origins. Control of their location and firing defines the uneven spatiotemporal program of replication in vertebrates. Despite extensive knowledge of the proteins involved, the exact structure of replication origins, as defined by the complex interactions between cis-determinants and regulatory protein factors, has not yet been fully unraveled. Single cell analyses of replication timing patterns brought to light a very well controlled program suggesting a tight regulation on initiation sites[1,2]. A crucial discovery of the past few years has been to demonstrate that Putative G-Quadruplex forming Sequences (PQSs) were functionally associated with replication origins [3–5]. Our group pioneered in showing PQS essentiality on model origins [6]. Recent studies using genome editing methods show that efficient initiation sites associated with transcriptional activity can synergize over several tens of kb by establishing physical contacts and lead to the formation of early domains of DNA replication demonstrating a co-regulation between replication initiation and transcription[7]. Studying one model origin in DT40 chicken cells, we recently showed that a dimeric PQS (ie two PQSs on the same strand) forms a minimal combination of cis-elements, necessary and sufficient for replication initiation. The within-tandem distance between PQS is flexible (23-111 bp) whereas the similar strand orientation is mandatory. This new nucleic acid feature (dimeric PQS) is associated with half of strong replication initiation sites genome-wide in human, mouse and chicken and directs the recruitment of the histone variant H2A.Z and the formation of a Nucleosome Free Region (NFR). Dimeric PQSs are therefore essential for the establishment of DNA replication programs (Poulet-Benedetti et al, in preparation).

1. Duriez, B., Chilaka, S., Bercher, J.-F., Hercul, E., & Prioleau, M.-N. (2019). Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase. Nucleic Acids Research, 47(10), 5155–5169. https://doi.org/10.1093/nar/gkz220

2. Takahashi, S., Miura, H., Shibata, T., Nagao, K., Okumura, K., Ogata, M., Obuse, C., Takebayashi, S.-I., & Hiratani, I. (2019). Genome-wide stability of the DNA replication program in single mammalian cells. Nature Genetics, 51(3), 529–540. https://doi.org/10.1038/s41588-019-0347-5

3. Besnard, E., Babled, A., Lapasset, L., Milhavet, O., Parrinello, H., Dantec, C., Marin, J.-M., & Lemaitre, J.-M. (2012). Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nature Structural & Molecular Biology, 19(8), 837–844. https://doi.org/10.1038/nsmb.2339

4. Cayrou, C., Coulombe, P., Puy, A., Rialle, S., Kaplan, N., Segal, E., & Méchali, M. (2012). New insights into replication origin characteristics in metazoans. Cell Cycle (Georgetown, Tex.), 11(4), 658–667. https://doi.org/10.4161/cc.11.4.19097

5. Picard, F., Cadoret, J.-C., Audit, B., Arneodo, A., Alberti, A., Battail, C., Duret, L., & Prioleau, M.-N. (2014). The Spatiotemporal Program of DNA Replication Is Associated with Specific Combinations of Chromatin Marks in Human Cells. PLoS Genet, 10(5), e1004282. https://doi.org/10.1371/journal.pgen.1004282

6. Valton, A.-L., Hassan-Zadeh, V., Lema, I., Boggetto, N., Alberti, P., Saintomé, C., Riou, J.-F., & Prioleau, M.-N. (2014). G4 motifs affect origin positioning and efficiency in two vertebrate replicators. The EMBO Journal, 33(7), 732–746. https://doi.org/10.1002/embj.201387506

7. Brossas, C., Valton, A.-L., Venev, S. V., Chilaka, S., Counillon, A., Laurent, M., Goncalves, C., Duriez, B., Picard, F., Dekker, J., & Prioleau, M.-N. (2020). Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. The EMBO Journal, 39(21), e99520. https://doi.org/10.15252/embj.201899520