Involvement of G-quadruplex regions in mammalian replication origin activity

Prorok, Paulina; Artufel, Marie; Aze, Antoine; Coulombe, Philippe; Peiffer, Isabelle; Lacroix, Laurent; Guédin, Aurore; Mergny, Jean‐Louis; Damaschke, Julia; Schepers, Aloys; Cayrou, Christelle; Teulade‐Fichou, Marie‐Paule; Ballester, Benoît; Méchali, Marcel

doi:10.1038/s41467-019-11104-0

Cited by 144 publications

(123 citation statements)

References 65 publications

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“…In addition to telomeres and pericentric heterochromatin, ATRX helps to resolve G-quadruplex (G4) structures in the DNA by deposition of H3.3 at those sites across the genome 5,33 . This is important because G4 structures can inhibit DNA replication and transcription 33,34 . G4 structures often overlap with noncanonical DNA:RNA hybrids called R-loops because both structures are favored in G-rich regions of the genome under negative torsional tension (e.g., active promoters) 35,36 .…”

Section: Resultsmentioning

confidence: 99%

MYCN amplification and ATRX mutations are incompatible in neuroblastoma

et al. 2020

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Aggressive cancers often have activating mutations in growth-controlling oncogenes and inactivating mutations in tumor-suppressor genes. In neuroblastoma, amplification of the MYCN oncogene and inactivation of the ATRX tumor-suppressor gene correlate with high-risk disease and poor prognosis. Here we show that ATRX mutations and MYCN amplification are mutually exclusive across all ages and stages in neuroblastoma. Using human cell lines and mouse models, we found that elevated MYCN expression and ATRX mutations are incompatible. Elevated MYCN levels promote metabolic reprogramming, mitochondrial dysfunction, reactive-oxygen species generation, and DNA-replicative stress. The combination of replicative stress caused by defects in the ATRX-histone chaperone complex, and that induced by MYCN-mediated metabolic reprogramming, leads to synthetic lethality. Therefore, ATRX and MYCN represent an unusual example, where inactivation of a tumorsuppressor gene and activation of an oncogene are incompatible. This synthetic lethality may eventually be exploited to improve outcomes for patients with high-risk neuroblastoma.

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Section: Resultsmentioning

confidence: 99%

MYCN amplification and ATRX mutations are incompatible in neuroblastoma

et al. 2020

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“…Thus, it is possible that the order by which each of these modifications is deposited during the cell cycle is a major determinant of the DNA synthesis initiation outcomes around them. Like in other eukaryotes (52,79,80), the specific arrangement of G4s around the sites of replication initiation may also be relevant, not only for the kinetics of these forms of chromatin deposition, but also other unknown epigenetic markers and replication-associated factors. Correlation between transcription and GC and AT skews in trypanosomatids has been reported before (28,51) and is mainly a consequence of constitutive transcription in these organisms.…”

Section: Discussionmentioning

confidence: 99%

Genome duplication inLeishmania majorrelies on DNA replication outside S phase

Damasceno

Marques

Beraldi

et al. 2019

Preprint

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Once every cell cycle, DNA replication takes place to allow cells to duplicate their genome and segregate the two resulting copies into offspring cells. In eukaryotes, the number of DNA replication initiation loci, termed origins, is proportional to chromosome size. However, previous studies have suggested that in Leishmania, a group of single-celled eukaryotic parasites, DNA replication starts from just a single origin per chromosome, which is predicted to be insufficient to secure complete genome duplication within S phase.Here, we show that the paucity of origins activated in early S phase is balanced by DNA synthesis activity outside S phase. Simultaneous recruitment of acetylated histone H3 (AcH3), modified base J and the kinetochore factor KKT1 is exclusively found at the origins used in early S phase, while subtelomeric DNA replication can only be linked to AcH3 and displays persistent activity through the cell cycle, including in G2/M and G1 phases. We also show that subtelomeric DNA replication, unlike replication from the previously mapped origins, is sensitive to hydroxyurea and dependent on subunits of the 9-1-1 complex.Our work indicates that Leishmania genome transmission relies on an unconventional DNA replication programme, which may have implications for genome stability in this important parasite. sequence read depth in the former relative to the latter. As result, DNA synthesis very late in S-phase, or that occurs outside of S-phase, would escape detection. To test this, we modified the MFA-seq approach in order that DNA content enrichment could be calculated in replicating cells relative to naturally occurring non-replicative cells. Mapping origins of replication by calculating DNA enrichment in exponentially growing cells versus cells in a stationary state has been used successfully in bacteria (42) and yeast (43). Thus, we reasoned that L. major in stationary phase could also serve as a non-replicative control for normalization in MFA-seq analysis compared with cells that are growing exponentially. To test this, we used flow cytometry to compare DNA content of exponentially growing and stationary phase cells and, in addition, compared the capacity of the two cell populations to incorporate the thymidine analogue 5-ethynyl-2'deoxyuridine (EdU; Fig. 1A,B). Flow cytometry showed that the proportion of cells in S phase (with DNA content between 1C and 2C) was substantially lower in a population of stationary cells compared with exponentially growing cells (Fig. 1A). Concomitantly, stationary phase cells, unlike exponentially growing cells, failed to incorporate EdU, even upon relatively long periods of incubation ( Fig. 1B). Thus, L. major cells in stationary phase do not perform any detectable DNA synthesis and were therefore deemed suitable to be used as the non-replicative sample in MFA-seq analysis.Next, we compared MFA-seq profiles using read depth ratios from FACS-sorted early S (ES) and G2 cells, and from exponentially growing cells (EXP) and stationary (STA) cells (Fig. 1C). As reported ...

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“…In line with this hypothesis, G4 motifs were first identified at telomeres, which are typically GC rich regions [78]. In addition, G4s were found within promoters of oncogenes [79,80], at replication origins [81] and CpG islands [82]. The importance of these sequences in numerous physiological processes is now becoming increasingly clear.…”

Section: Int J Mol Sci 2020 21 X For Peer Review 11 Of 28mentioning

confidence: 78%

From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork

Maffia

Ranise

Sabbioneda

2020

IJMS

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Replicating the entire genome is one of the most complex tasks for all organisms. Research carried out in the last few years has provided us with a clearer picture on how cells preserve genomic information from the numerous insults that may endanger its stability. Different DNA repair pathways, coping with exogenous or endogenous threat, have been dissected at the molecular level. More recently, there has been an increasing interest towards intrinsic obstacles to genome replication, paving the way to a novel view on genomic stability. Indeed, in some cases, the movement of the replication fork can be hindered by the presence of stable DNA: RNA hybrids (R-loops), the folding of G-rich sequences into G-quadruplex structures (G4s) or repetitive elements present at Common Fragile Sites (CFS). Although differing in their nature and in the way they affect the replication fork, all of these obstacles are a source of replication stress. Replication stress is one of the main hallmarks of cancer and its prevention is becoming increasingly important as a target for future chemotherapeutics. Here we will try to summarize how these three obstacles are generated and how the cells handle replication stress upon their encounter. Finally, we will consider their role in cancer and their exploitation in current chemotherapeutic approaches.

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Involvement of G-quadruplex regions in mammalian replication origin activity

Cited by 144 publications

References 65 publications

MYCN amplification and ATRX mutations are incompatible in neuroblastoma

MYCN amplification and ATRX mutations are incompatible in neuroblastoma

Genome duplication inLeishmania majorrelies on DNA replication outside S phase

From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork

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