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

Mar 8, 2021

Open access
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Abstract
Data availability
Article and author information
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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

(2020) Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones
ENA European Nucleotide Archive, PRJEB32855.

https://www.ebi.ac.uk/ena/browser/view/PRJEB32855

The following previously published data sets were used

(2019) RNA-seq in Raji cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycycline
ENA European Nucleotide Archive, PRJEB31867.

https://www.ebi.ac.uk/ena/browser/view/PRJEB31867
1. Wu X
2. Kabalane H
3. Kahli M
4. Petryk N
5. Laperrousaz B
6. Jaszczyszyn Y
7. Drillon G
8. Nicolini FE
9. Perot G
10. Robert A
11. Fund C
12. Chibon F
13. Xia R
14. Wiels J
15. Argoul F
16. Maguer-Satta V
17. Arneodo A
18. Audit B
19. Hyrien O.
(2018) Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions.
ENA European Nucleotide Archive, PRJEB25180.

https://www.ebi.ac.uk/ena/browser/view/PRJEB25180
(2018) Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors [repli-seq]
NCBI Gene Expression Omnibus, GSE102522.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102522
1. Petryk
2. N.
3. Dalby
4. M.
5. Wenger
6. A.
7. Stromme
8. C. B.
9. Strandsby
10. A.
11. Andersson
12. R.
13. & Groth
14. A.
(2018) MCM2 promotes symmetric inheritance of modified histones during DNA replication
ENA European Nucleotide Archive, SRR7535256.

https://www.ebi.ac.uk/ena/browser/view/SRR7535256
1. Tubbs
2. A.
3. Sridharan
4. S.
5. van Wietmarschen
6. N.
7. Maman
8. Y.
9. Callen
10. E.
11. Stanlie
12. A.
13. Wu
14. W.
15. Wu
16. X.
17. Day
18. A.
19. Wong
20. N.
21. Yin
22. M.
23. Canela
24. A.
25. Fu
26. H.
27. Redon
28. C.
29. Pruitt
30. S. C.
31. Jaszczyszyn
32. Y.
33. Aladjem
34. M. I.
35. Aplan
36. P. D.
37. Hyrien
38. O.
39. & Nussenzweig
40. A.
(2018) OK-seq profile from cycling (S) phase untreated B cells
NCBI Gene Expression Omnibus, GSE116319.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116319

Article and author information

Author details

Nina Kirstein

Department of Gene Vectors, Helmholtz Zentrum München (GmbH), München, Germany

Competing interests
The authors declare that no competing interests exist.
Alexander Buschle

Department of Gene Vectors, Helmholtz Zentrum München (GmbH), München, Germany

Competing interests
The authors declare that no competing interests exist.
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.
Stefan Krebs

Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany

Competing interests
The authors declare that no competing interests exist.
Helmut Blum

Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany

Competing interests
The authors declare that no competing interests exist.
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.
Ina M Vorberg

Deutsches Zentrum für Neurodegenerative Erkrankungen, Bonn, Germany

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0583-4015
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.

"This ORCID iD identifies the author of this article:" 0000-0002-4659-0427
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.
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.

"This ORCID iD identifies the author of this article:" 0000-0001-8879-675X
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.

"This ORCID iD identifies the author of this article:" 0000-0003-2683-9990
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.

"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.

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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.