Chromosomal Domains and DNA Replication

MARIE-NOËLLE PRIOLEAU

During development, chromosomal domains of expression are structured as cells actively divide. Before each division, cells must copy their genome as accuratly as possible or risk cell death or genomic instability leading to the establishment of cancer cells. This process is called DNA replication and starts at multiple specific sites (~100,000 in humans), called origins of replication. A spatiotemporal program controls the positioning and the activation time of the origins of replication during the S phase of the cell cycle. The goal of the team is to identify the molecular mechanisms that implement this program. More recently, we are also trying to understand how two fundamental processes, transcription and replication, act on the same molecule simultaneously in the most harmonious way possible. Indeed, it is now clearly established that conflicts between these two machineries can be a source of genomic instability.

Key words : DNA replication, G-quadruplex, Chromatin, Commun Fragile Sites, Cortical Organoïd.

+33 (0)157278102     marie-noelle.prioleau(at)ijm.fr     @MariePrioleau

In order to get a general view of human genome replication, we are developing high-throughput analyses to map the origins of replication as well as their activation time (Figure 1).

 

Figure 1. Representative features of early and late replication domains

UCSC genome browser visualization of a 3Mb genomic region of the avian chromosome 1. Data were obtained in the DT40 avian cell line. Tracks of nascent strands (NS) enrichments in the four S-phase fractions, from early to late, are shown separately (S1 to S4). NS-enriched and depleted regions for each fraction are shown in red and blue, respectively. This data provides information on the temporal program of DNA replication. Single reads from nascent RNA-seq data and aligned SNS (spatial program of DNA replication) are reported and between tracks of annotated genes (RefSeq genes) and CpG Islands. The bottom track shows GC content (GC percent).

 

Collaboration with statisticians and bioinformaticians has allowed us to link these maps to genomic data on chromatin structure and gene expression. We also use an avian cell model (the DT40 cell line) which has the unique property of performing homologous recombination very efficiently. This powerful genetic model allows us to test very efficiently different hypotheses extracted from genomic analyses. We were able to show that G-quadruplexes play a key role in the definition of replication origins. We have just identified a complex motif that is found in half of the strong origins in humans, mice and chickens. Future projects will focus on understanding how this motif ensures the efficient recruitment of the replication machinery.

 

In a second line of research, we are analyzing how the origin signal carried by this complex motif interacts with the transcription process that takes place on the same substrate, DNA. These analyses will allow us to test a well-supported hypothesis that transcription is able to shift the starting points of replication and thus generally promote replication initiation in intergenic regions. Common Fragile Sites (CFSs) are recurrent sites of chromosomal rearrangements in cancers and some neurological diseases. They are found within large (> 300 kb) genes transcribed and replicated at the end of S phase. One hypothesis regarding their formation is that the lack of replication initiation events along these genes results in incomplete replication of these regions before mitosis. Transcription would remove the pre-replication complexes located within the bodies of these genes, thus inducing a depletion of replication origins. We seek to test the ability of RNA polymerase II to displace pre-replication complexes by inserting a strong or inducible promoter upstream of a highly efficient minimal model origin lacking transcriptional activity. This project will explore an important hypothesis on the formation of CFS. In the longer term, we will test the hypothesis that recurrent break sites observed during the proliferation of neuronal precursors have the characteristic properties of CFS. For this purpose, we will use human brain organoids as a model system.

 

The understanding of the duplication mode of eukaryotic genomes is essential. Indeed, replication not only ensures the maintenance of genome integrity, but also coordinates the establishment of expression programs during development.

Group Leader:

Marie-Noëlle PRIOLEAU
Téléphone : +33 (0)157278102
Email : marie-noelle.prioleau(at)ijm.fr

 

Members :

Caroline BROSSAS Biological engineer
Juliette MANDELBROJT PhD Student

1) Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. Brossas C, Valton AL, Venev SV, Chilaka S, Counillon A, Laurent M, Goncalves C, Duriez B, Picard F, Dekker J, Prioleau MN. EMBO J. 2020 Nov 2;39(21):e99520. doi: 10.15252/embj.201899520. Epub 2020 Sep 16. PMID: 32935369

2) Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase. Duriez B, Chilaka S, Bercher JF, Hercul E, Prioleau MN. Nucleic Acids Res. 2019 Jun 4;47(10):5155-5169. doi: 10.1093/nar/gkz220. PMID: 30926993

3) Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints. Massip F, Laurent M, Brossas C, Fernández-Justel JM, Gómez M, Prioleau MN, Duret L, Picard F. Nucleic Acids Res. 2019 Jun 4;47(10):5114-5125. doi: 10.1093/nar/gkz182. PMID: 30916335

4) Transcription-dependent regulation of replication dynamics modulates genome stability. Blin M, Le Tallec B, Nähse V, Schmidt M, Brossas C, Millot GA, Prioleau MN, Debatisse M. Nat Struct Mol Biol. 2019 Jan;26(1):58-66. doi: 10.1038/s41594-018-0170-1. Epub 2018 Dec 31. PMID: 30598553

5) The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells. Picard F, Cadoret JC, Audit B, Arneodo A, Alberti A, Battail C, Duret L, Prioleau MN. PLoS Genet. 2014 May 1;10(5):e1004282. doi: 10.1371/journal.pgen.1004282. eCollection 2014 May. PMID: 24785686

6) G4 motifs affect origin positioning and efficiency in two vertebrate replicators. Valton AL, Hassan-Zadeh V, Lema I, Boggetto N, Alberti P, Saintomé C, Riou JF, Prioleau MN. EMBO J. 2014 Apr 1;33(7):732-46. doi: 10.1002/embj.201387506. Epub 2014 Feb 12. PMID: 24521668

7) USF binding sequences from the HS4 insulator element impose early replication timing on a vertebrate replicator. Hassan-Zadeh V, Chilaka S, Cadoret JC, Ma MK, Boggetto N, West AG, Prioleau MN. PLoS Biol. 2012;10(3):e1001277. doi: 10.1371/journal.pbio.1001277. Epub 2012 Mar 6. PMID: 22412349

8) Genome-wide studies highlight indirect links between human replication origins and gene regulation. Cadoret JC, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, Duret L, Quesneville H, Prioleau MN. Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15837-42. doi: 10.1073/pnas.0805208105. Epub 2008 Oct 6. PMID: 18838675

9) Broadening of DNA replication origin usage during metazoan cell differentiation. Dazy S, Gandrillon O, Hyrien O, Prioleau MN. EMBO Rep. 2006 Aug;7(8):806-11. doi: 10.1038/sj.embor.7400736. Epub 2006 Jun 16. PMID: 16799461

10) Replication of the chicken beta-globin locus: early-firing origins at the 5′ HS4 insulator and the rho- and betaA-globin genes show opposite epigenetic modifications. Prioleau MN, Gendron MC, Hyrien O. Mol Cell Biol. 2003 May;23(10):3536-49. doi: 10.1128/MCB.23.10.3536-3549.2003. PMID: 12724412

Since 2015 :

  • Promoters are key organizers of the duplication of vertebrate genomes. Brossas C, Duriez B, Valton AL, Prioleau MN. Bioessays. 2021 Oct;43(10):e2100141. doi: 10.1002/bies.202100141. Epub 2021 Jul 28. PMID: 34319621 Review.
  • Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. Brossas C, Valton AL, Venev SV, Chilaka S, Counillon A, Laurent M, Goncalves C, Duriez B, Picard F, Dekker J, Prioleau MN. EMBO J. 2020 Nov 2;39(21):e99520. doi: 10.15252/embj.201899520. Epub 2020 Sep 16. PMID: 32935369 Free PMC article.
  • Des mécanismes moléculaires aux applications cliniques. L’essentiel du Colloque Réplication-Réparation-Recombinaison 2019. Lambert S, Borde V, Charbonnier JB, Dantzer F, Espéli O, Guirouilh-Barbat J, Llorente B, Legube G, Prioleau MN, Radicella P. Bull Cancer. 2020 Feb;107(2):283-287. doi: 10.1016/j.bulcan.2020.01.003. Epub 2020 Jan 31. PMID: 32014246 French. No abstract available.
  • Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase. Duriez B, Chilaka S, Bercher JF, Hercul E, Prioleau MN. Nucleic Acids Res. 2019 Jun 4;47(10):5155-5169. doi: 10.1093/nar/gkz220. PMID: 30926993 Free PMC article.
  • Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints. Massip F, Laurent M, Brossas C, Fernández-Justel JM, Gómez M, Prioleau MN, Duret L, Picard F. Nucleic Acids Res. 2019 Jun 4;47(10):5114-5125. doi: 10.1093/nar/gkz182. PMID: 30916335 Free PMC article.
  • Transcription-dependent regulation of replication dynamics modulates genome stability. Blin M, Le Tallec B, Nähse V, Schmidt M, Brossas C, Millot GA, Prioleau MN, Debatisse M. Nat Struct Mol Biol. 2019 Jan;26(1):58-66. doi: 10.1038/s41594-018-0170-1. Epub 2018 Dec 31. PMID: 30598553
  • G-Quadruplexes and DNA Replication Origins. Prioleau MN. Adv Exp Med Biol. 2017;1042:273-286. doi: 10.1007/978-981-10-6955-0_13. PMID: 29357063 Review.
  • [G-quadruplex: key controllers of human genome duplication]. Poulet-Benedetti J, Valton AL, Prioleau MN. Med Sci (Paris). 2017 Dec;33(12):1063-1070. doi: 10.1051/medsci/20173312013. Epub 2017 Dec 20. PMID: 29261494 Free article. Review. French.
  • G-Quadruplexes in DNA Replication: A Problem or a Necessity? Valton AL, Prioleau MN. Trends Genet. 2016 Nov;32(11):697-706. doi: 10.1016/j.tig.2016.09.004. Epub 2016 Sep 20. PMID: 27663528 Review.
  • DNA replication origins-where do we begin? Prioleau MN, MacAlpine DM. Genes Dev. 2016 Aug 1;30(15):1683-97. doi: 10.1101/gad.285114.116. PMID: 27542827 Free PMC article. Review.

« Rôle de l’insulateur 5’HS4 du poulet dans la régulation de la réplication » soutenue en Juin 2009 par Vahideh Hassan-Zadeh.

– « Mécanismes moléculaires de l’initiation de la réplication » soutenue en Décembre 2010 par Françoise Meisch.

– « Identification de séquences cis-nucléiques nécessaires à l’initiation de la réplication chez les vertébrés » soutenue en Juin 2014 par Anne-Laure Valton.

– « Construction d’un domaine synthétique de réplication précoce et impact sur la structure chromatinienne et la permissivité transcriptionnelle » soutenue en Septembre 2015 par Caroline Tonnerre-Doncarli Brossas.

– « Mécanismes moléculaires impliqués dans la régulation du moment de déclenchement des origines de réplication » soutenue en Novembre 2016 par Antonin Counillon.

– « Rôle des G-quadruplexes dans la spécification des origines de réplication chez les vertébrés » soutenue en Septembre 2016 par Marc Laurent.

– « Etude moléculaire des éléments cis-régulateurs et de l’organisation de la chromatine des origines de réplication » soutenue en Septembre 2020 par Jérémy Poulet-Benedetti.

Nationales :

– Imagerie cellulaire et cytométrie en flux : Plateforme Imago-Seine, Institut Jacques Monod

– Organoïdes corticaux : Plateforme enSCORE, Labex Who am I ?

– Bio-informatique et bio-statistique : LBBE, UCB Lyon 1 (Laurent Duret) et ENS de Lyon (Franck Picard)

– G-quadruplex : Inserm U565, CNRS UMR 7196, MNHN, Paris, France (Patrizia Alberti, Carole Saintomé et Jean-François Riou)

– Sites Fragiles Communs : : Institut Gustave Roussy, Villejuif (Michelle Debatisse et Stéphane Koundrioukoff)

 

Internationales :

– Organisation tri-dimensionnelle du noyau : University of Massachusetts Medical School, Worcester, Etats-Unis (Anne-Laure Valton et Job Dekker)

– Rôle des G4s dans le positionnement des nucléosomes : Fox Chase Cancer center, Philadelphie, Etats-Unis et Moscow State University, Moscow, Russie (Vasily Studitsky).