1. Chromosomes and Gene Expression

Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones

  1. Nina Kirstein
  2. Alexander Buschle
  3. Xia Wu
  4. Stefan Krebs
  5. Helmut Blum
  6. Elisabeth Kremmer
  7. Ina M Vorberg
  8. Wolfgang Hammerschmidt
  9. Laurent Lacroix
  10. Olivier Hyrien  Is a corresponding author
  11. Benjamin Audit  Is a corresponding author
  12. Aloys Schepers  Is a corresponding author
  1. Helmholtz Zentrum München (GmbH), Germany
  2. INSERM, France
  3. Gene Center, LMU Munich, Germany
  4. Helmholtz Zentrum Munich, Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH), Germany
  5. Deutsches Zentrum für Neurodegenerative Erkrankungen, Germany
  6. Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Germany
  7. Inserm, France
  8. Institut de Biologie de l'Ecole Normale Supérieure, France
  9. CNRS, Ecole Normale Supérieure de Lyon, France
https://doi.org/10.7554/eLife.62161
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Cite this article
  1. Nina Kirstein
  2. Alexander Buschle
  3. Xia Wu
  4. Stefan Krebs
  5. Helmut Blum
  6. Elisabeth Kremmer
  7. Ina M Vorberg
  8. Wolfgang Hammerschmidt
  9. Laurent Lacroix
  10. Olivier Hyrien
  11. Benjamin Audit
  12. Aloys Schepers
(2021)
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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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

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Nina Kirstein

    Department of Gene Vectors, Helmholtz Zentrum München (GmbH), München, Germany
    Competing interests
    The authors declare that no competing interests exist.

  2. Alexander Buschle

    Department of Gene Vectors, Helmholtz Zentrum München (GmbH), München, Germany
    Competing interests
    The authors declare that no competing interests exist.

  3. Xia Wu

    Institut de Biologie de l'ENS (IBENS), Departement de Biologie, Ecole Normale Superieure, CNRS, Inserm, PSL Research University, INSERM, Paris, France
    Competing interests
    The authors declare that no competing interests exist.

  4. Stefan Krebs

    Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
    Competing interests
    The authors declare that no competing interests exist.

  5. Helmut Blum

    Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
    Competing interests
    The authors declare that no competing interests exist.

  6. Elisabeth Kremmer

    Institue of Immonolgy, Helmholtz Zentrum Munich, Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH), Muenchen, Germany
    Competing interests
    The authors declare that no competing interests exist.

  7. Ina M Vorberg

    Deutsches Zentrum für Neurodegenerative Erkrankungen, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0583-4015

  8. Wolfgang Hammerschmidt

    Research Unit Gene Vectors, Helmholtz Zentrum München, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4659-0427

  9. Laurent Lacroix

    Institut de Biologie de l'ENS (IBENS), Departement de Biologie, Ecole Normale Superieure, CNRS, Inserm, PSL Research University, Inserm, Paris, France
    Competing interests
    The authors declare that no competing interests exist.

  10. Olivier Hyrien

    Institut de Biologie de l'Ecole Normale Supérieure, Paris, France
    For correspondence
    hyrien@biologie.ens.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8879-675X

  11. Benjamin Audit

    Laboratoire de Physique, ENS de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Lyon, France
    For correspondence
    benjamin.audit@ens-lyon.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2683-9990

  12. Aloys Schepers

    Department of Gene Vectors, Helmholtz Zentrum Munich, Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH), Muenchen, Germany
    For correspondence
    schepers@helmholtz-muenchen.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5442-5608

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.

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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  1. Nina Kirstein
  2. Alexander Buschle
  3. Xia Wu
  4. Stefan Krebs
  5. Helmut Blum
  6. Elisabeth Kremmer
  7. Ina M Vorberg
  8. Wolfgang Hammerschmidt
  9. Laurent Lacroix
  10. Olivier Hyrien
  11. Benjamin Audit
  12. Aloys Schepers
(2021)
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

Share this article

https://doi.org/10.7554/eLife.62161

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