Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones
- Helmholtz Zentrum München (GmbH), Germany
- INSERM, France
- Gene Center, LMU Munich, Germany
- Helmholtz Zentrum Munich, Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH), Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Germany
- Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Germany
- Inserm, France
- Institut de Biologie de l'Ecole Normale Supérieure, France
- CNRS, Ecole Normale Supérieure de Lyon, France
Abstract
Eukaryotic DNA replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with gene expression, replication timing and fork directionality profiles obtained by RNA-seq, Repli-seq and OK-seq. ORC and MCM are significantly and homogeneously depleted from transcribed genes, enriched at gene promoters, and more abundant in early- than in late-replicating domains. Surprisingly, after controlling these variables, no difference in ORC/MCM density is detected between initiation zones, termination zones, unidirectionally replicating and randomly replicating regions. Therefore, ORC/MCM density correlates with replication timing but does not solely regulate the probability of replication initiation. Interestingly, H4K20me3, a histone modification proposed to facilitate late origin licensing, was enriched in late replicating initiation zones and gene deserts of stochastic replication fork direction. We discuss potential mechanisms specifying when and where replication initiates in human cells.
Data availability
Sequencing data have been deposited ad the ENA European Nucleotide Archive and NCBI Gene Expression Omnibus as indicatedChIP-Seq: PRJEB32855, RNA-seq Raji: PRJEB31867 OK-seq Raji: PRJEB25180, Repli-seq Raji: GSE102522, OK-seq mESC: SRR,7535256, OK-seq mouse B-cells: GSE116319All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1-6; Fig. 1-Fig.1-Suppl. 3; Fig2-Fig2 Suppl. 1,2; Fig3-Fig3-Suppl. 1; Fig. 4-Fig.4 Suppl. 1,2; Fig5-Fig.5-Suppl. 1; Fig7-Fig.7-Suppl. 1
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Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zonesENA European Nucleotide Archive, PRJEB32855.
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RNA-seq in Raji cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycyclineENA European Nucleotide Archive, PRJEB31867.
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MCM2 promotes symmetric inheritance of modified histones during DNA replicationENA European Nucleotide Archive, SRR7535256.
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OK-seq profile from cycling (S) phase untreated B cellsNCBI Gene Expression Omnibus, GSE116319.
Article and author information
Author details
Wolfgang Hammerschmidt
Funding
Helmholtz Zentrum Muenchen
- Nina Kirstein
- Alexander Buschle
- Wolfgang Hammerschmidt
- Aloys Schepers
National Cancer Institute (CA70723)
- Wolfgang Hammerschmidt
Deutsche Forschungsgemeinschaft (SFB 1064 TP05; SFB1064/TP A13,SFB-TR36/TP A04)
- Wolfgang Hammerschmidt
- Aloys Schepers
Agence Nationale de la Recherche (ANR-15-CE12-0011,ANR-18-CE45-0002,ANR-19-CE12-0028,ANR-10-IDEX-0001-02)
- Olivier Hyrien
- Benjamin Audit
Fondation pour la Recherche Médicale (FRM DEI201512344404)
- Olivier Hyrien
- Benjamin Audit
Canceropole Ile-de-France (PL-BIO16-302)
- Olivier Hyrien
- Benjamin Audit
INCa
- Olivier Hyrien
Ligue Nationale Contre le Cancer (RS19/75-75)
- Olivier Hyrien
Association pour la Recherche sur le Cancer (PJA 20171206387)
- Olivier Hyrien
Deutsche Krebshilfe (70112875)
- Wolfgang Hammerschmidt
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Bruce Stillman, Cold Spring Harbor Laboratory, United States
Version history
- Received: August 16, 2020
- Accepted: March 5, 2021
- Accepted Manuscript published: March 8, 2021 (version 1)
- Version of Record published: March 24, 2021 (version 2)
Copyright
© 2021, Kirstein et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones
eLife 10:e62161.
https://doi.org/10.7554/eLife.62161
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