Histone H4K20 methylation mediated chromatin compaction threshold ensures genome integrity by limiting DNA replication licensing

Shoaib, Muhammad; Walter, David; Gillespie, Peter P.J.; Izard, Fanny; Fahrenkrog, Birthe; Llères, David; Lerdrup, Mads; Johansen, Jens Vilstrup; Hansen, Klaus; Julien, Éric; Blow, J. Julian; Sørensen, Claus Storgaard

doi:10.1038/s41467-018-06066-8

Cited by 86 publications

(99 citation statements)

References 65 publications

(68 reference statements)

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“…We show that H4K20me3 is present in a subset of non-genic late replicating initiation zones, which are enriched in ORC/ MCM binding. This confirms our previous finding that H4K20me3-mediated ORC-DNA binding enhances origin activity in certain environments 18, 32 . Finally, we find that the global density of ORC highly correlates with replication timing, an effect observed less prominently for MCM.…”

supporting

confidence: 92%

“…H4K20 methylation has multiple functions in ensuring genome integrity, such as DNA replication 39, 45, 46 , DNA damage repair, and chromatin compaction 32, 47, 48 suggesting that the different functions are context dependent and executed with different players. We previously demonstrated that H4K20me3 provides a platform to enhance origin formation in late replicating heterochromatin 18 .…”

Section: Discussionmentioning

confidence: 99%

“…We previously demonstrated that H4K20me3 provides a platform to enhance origin formation in late replicating heterochromatin 18 . Shoaib and colleagues reported recently that H4K20me3 restricts replication licensing to prevent overreplication 32 . The latter is in line with our observation that mainly ORC but little MCM are enriched at H4K20me3 peaks (Fig.…”

Section: Discussionmentioning

confidence: 99%

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Active transcription regulates ORC/MCM distribution whereas replication timing correlates with ORC density in human cells

Kirstein¹,

Buschle²,

Wu³

et al. 2019

Preprint

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42Eukaryotic replication initiates during S phase from origins that have been licensed in 43 the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors 44Orc2, Orc3, Mcm3, and Mcm7 with replication initiation events obtained by Okazaki 45 fragment sequencing. We demonstrate that MCM is displaced from early replicating, 46 actively transcribed gene bodies, while ORC is mainly enriched at active TSS. Late 47Mammalian DNA replication is a highly orchestrated process ensuring the 55 exact inheritance of genomes of tens to thousands of million base pairs in size. In 56 human cells, replication initiates from 30,000 -50,000 replication origins per cell 1,2 . 57 Origins are not activated synchronously but are organized into individual replication 58 timing domains (RTDs), which replicate in a timely coordinated and reproducible 59 order from early to late in S phase 3,4 . The replication cascade or domino model 60 proposes that within one RTD, replication first initiates at the most efficient origins 61 and then spreads to less efficient origins. RTDs are separated by timing transition 62 regions and it is debated whether replication spreading is blocked at these regions 5,6 . 63The establishment of replication competence occurs in late mitosis and during 64 the G1 phase of the cell cycle 7 . The first step is the cell-cycle dependent assembly of 65 the evolutionary conserved origin recognition complex (ORC) to origins 8,9 . ORC and 66 two chaperones, Cdt1 and Cdc6, cooperatively load minichromosome maintenance 67 (MCM) complexes as double hexamers 10-12 . The MCM complex is the central unit of 68 the replicative helicase. The resulting multi-subunit complex is termed pre-replicative 69 complex (pre-RC). A single ORC loads multiple MCM helicases, which are 70 translocated from their original loading site, but no ORC, neither Cdc6, nor Cdt1 are 71 required for origin activation 13,14 . 72Replication origins are defined functionally. In the unicellular S. cerevisiae, 73 replication origins are genetically characterized by the ARS consensus sequence 15 . In 74 multicellular organisms, replication initiates from flexible locations and no common 75 consensus element for origin selection and activation has yet been identified. It is 76 generally believed that chromatin features including histone modifications, 77 nucleosome dynamics and DNA modifications contribute to origin specification 1,16,17 , 78 including H4K20me3 that supports the licensing of a subset of late replicating origins in heterochromatin 18 . Thus, changing environmental conditions, DNA damage and the 80 development status of each cell are integrated into highly dynamic local chromatin 81 profiles, which influence the plasticity of origin selection 1 . 82 Different approaches have been developed to characterize mammalian 83 replication initiation by single-molecule visualization (DNA combing) or sequencing 84 of purified initiation products (short nascent strands (SNS-seq), initiation site 85 sequencing (INI-seq) replicatio...

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supporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Active transcription regulates ORC/MCM distribution whereas replication timing correlates with ORC density in human cells

Kirstein¹,

Buschle²,

Wu³

et al. 2019

Preprint

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“…Few DNA breaks are generally sufficient to activate P53 functions 32,33 . Since the first impact of loss of SETD8 activity is excessive chromatin relaxation and progressive DNA damage after exit of mitosis 34 , we propose that the activation of p53 we detect in MM cells upon SETD8 inhibition is mainly triggered by cellular stresses during G1 progression. This would also explain why UNC0379mediated SETD8 inhibition is very toxic in P53-deficient MM cells, where the absence of a functional p53-mediated G1 arrest allows damaged cells to pursue into S-phase and accumulate a deadly level of DNA breaks, likely caused by improper replication fork progression 24 .…”

Section: Pharmacological Inhibition Of Setd8 Synergizes With Melphalamentioning

confidence: 86%

Targeting the methyltransferase SETD8 impairs tumor cell survival and overcomes drug resistance independently of p53 status in multiple myeloma

Herviou

Izard

Karmous-Gadacha³

et al. 2019

Preprint

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Multiple myeloma (MM) is a malignancy of plasma cells that largely remains incurable.The search for new therapeutic targets is therefore essential. Here we show that a higher expression of the lysine methyltransferase SETD8, which is responsible for histone H4K20 mono-methylation, is an adverse prognosis factor associated with a poor outcome in two cohorts of newly diagnosed patients. Remarkably, primary malignant plasma cells are particularly addicted to SETD8 activity. Indeed, pharmacological inhibition of this enzyme by the chemical compound UNC0379 demonstrated a significantly higher toxicity in MM cells compared to normal cells from the bone marrow microenvironment. Moreover, RNA sequencing and functional studies revealed that SETD8 inhibition induces a mature non-proliferating plasma cell signature and an activation of the p53 canonical pathway, which together leads to an impairment of myeloma cell proliferation and survival. However, UNC0379 treatment triggers a deadly level of replicative stress in p53 deficient MM cells, indicating that the cytotoxicity associated with SETD8 inhibition is independent of the p53 status. Consistent with this, the combination of UNC0379 with the conventional cytotoxic agent melphalan strongly enhances DNA damage and overcomes drug resistance in myeloma cells.Thus, targeting SETD8 could be of therapeutic interest to improve MM treatment in highrisk patients independently of the p53 status.3

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“…In a single-celled eukaryotic microbe like yeast, such a genome-scale effect could impinge on organismal fitness by reducing cell proliferation rates and/or genome stability, as delayed replication is associated with enhanced mutation frequency (45; 46). However, in mammalian cells, SirT1, the human ortholog of yeast Sir2, as well as Set8-mediated chromatin compaction limit origin function and promote genome stability (47; 48; 49). Notably, the Set-8 mechanism works at the level of limiting MCM binding to chromatin.…”

Section: Discussionmentioning

confidence: 99%

Sir2 mitigates an intrinsic imbalance in origin licensing efficiency between early and late replicating euchromatin

Hoggard

Müller

Nieduszynski

et al. 2020

Preprint

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1A eukaryotic chromosome relies on the function of multiple spatially distributed DNA replication origins for its stable inheritance. 2 The location of an origin is determined by the chromosomal position of an MCM complex, the inactive form of the DNA 3 replicative helicase that is assembled on chromosomal DNA in G1-phase (a.k.a. origin licensing). While the biochemistry 4 of origin licensing is understood, the mechanisms that promote an adequate spatial distribution of MCM complexes across 5 chromosomes are not. We have elucidated a role for the Sir2 histone deacetylase in establishing the normal distribution of 6 MCM complexes across Saccharomyces cerevisiae chromosomes. In the absence of Sir2, MCM complexes accumulated within 7 both early-replicating euchromatin and telomeric heterochromatin, and replication activity within these regions was enhanced. 8 Concomitantly, the duplication of several regions of late-replicating euchromatin were delayed. Thus, Sir2-mediated attenuation 9 of origin licensing established the normal spatial distribution of origins across yeast chromosomes required for normal genome 10 duplication. 11Significance statement 12 In eukaryotes, multiple DNA replication origins, the sites where new DNA synthesis begins during the process 13 of cell division, must be adequately distributed across chromosomes to maintain normal cell proliferation 14 and genome stability. This study describes a repressive chromatin-mediated mechanism that acts at the 15 level of individual origins to attenuate the efficiency of origin formation. This attenuation is essential for 16 achieving the normal spatial distribution of origins across the chromosomes of the eukaryotic microbe Sac-17 charomyces cerevisiae. While the importance of chromosomal origin distribution to cellular fitness is now 18 widely acknowledged, this study is the first to define a specific chromatin modification that establishes the 19 normal spatial distribution of origins across a eukaryotic genome. 21An adequate distribution of DNA replication origins across eukaryotic chromosomes is important for 22 maintaining cell proliferation and genome stability over the course of multiple rounds of cell division. mosomal regions that contain a paucity of origins are linked to chromosome fragility and cancer-associated 24 deletions (1; 2; 3; 4). Origin function relies on two distinct cell-cycle restricted reactions (5). In G1-phase, 25 the ORC (origin recognition complex) and Cdc6 protein bind DNA and direct the assembly of a stable 26 catalytically inactive MCM (minichromosome maintenance) complex, a.k.a. origin licensing. In S-phase, 27 kinases and accessory proteins act on the MCM complex to convert it into two bidirectionally oriented 28 replicative helicases that unwind the DNA to allow for new DNA synthesis (a.k.a. origin activation). Thus, 29 the effective chromosomal distribution of two distinct reactions, MCM complex loading and MCM complex 30 activation, establishes the normal spatiotemporal distribution of orig...

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Histone H4K20 methylation mediated chromatin compaction threshold ensures genome integrity by limiting DNA replication licensing

Cited by 86 publications

References 65 publications

Active transcription regulates ORC/MCM distribution whereas replication timing correlates with ORC density in human cells

Active transcription regulates ORC/MCM distribution whereas replication timing correlates with ORC density in human cells

Targeting the methyltransferase SETD8 impairs tumor cell survival and overcomes drug resistance independently of p53 status in multiple myeloma

Sir2 mitigates an intrinsic imbalance in origin licensing efficiency between early and late replicating euchromatin

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