Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Symmetric inheritance of parental histones contributes to safeguarding the fate of mouse embryonic stem cells during differentiation

Nature Genetics volume 55, pages 1555–1566 (2023)Cite this article

Subjects

Abstract

Parental histones, the carriers of posttranslational modifications, are deposited evenly onto the replicating DNA of sister chromatids in a process dependent on the Mcm2 subunit of DNA helicase and the Pole3 subunit of leading-strand DNA polymerase. The biological significance of parental histone propagation remains unclear. Here we show that Mcm2-mutated or Pole3-deleted mouse embryonic stem cells (ESCs) display aberrant histone landscapes and impaired neural differentiation. Mutation of the Mcm2 histone-binding domain causes defects in pre-implantation development and embryonic lethality. ESCs with biased parental histone transfer exhibit increased epigenetic heterogeneity, showing altered histone variant H3.3 and H3K27me3 patterning at genomic sites regulating differentiation genes. Our results indicate that the lagging strand pattern of H3.3 leads to the redistribution of H3K27me3 in Mcm2-2A ESCs. We demonstrate that symmetric parental histone deposition to sister chromatids contributes to cellular differentiation and development.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Mcm2-2A mutation alters the H3K27me3 landscape of ESCs.
Fig. 2: Mcm2-2A mutation impairs ESC differentiation and mouse development.
Fig. 3: Single-cell lineage and transcriptome sequencing maps distinct fate of NPCs differentiated from WT versus Mcm2-2A ESCs.
Fig. 4: Mcm2-2A mutation increases histone H3K27me3 heterogeneity.
Fig. 5: Mcm2-2A mutation increases cellular transcriptional heterogeneity.
Fig. 6: Mcm2-2A mutation forms superclones.
Fig. 7: H3.3 coordinates with H3K27me3 to impair Mcm2-2A ESC differentiation.

Similar content being viewed by others

Data availability

The datasets generated during and/or analyzed during the current study are available in the Expression Omnibus data base repository (GEO). The next-generation sequencing datasets (RNA-seq, scRNA-seq, CUT&Tag, scCUT&Tag, eSPAN, CUT&RUN, MINCE-seq, ATAC-seq and Repli-ATAC-seq) have been deposited in the GEO with accession GSE185271 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE185271). Publication ChIP-seq datasets used for comparison were downloaded from GEO (https://www.ncbi.nlm.nih.gov/geo/) under accession numbers GSM3267572 (H3.3, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3267572), GSM2345017 (H3.3, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2345017), GSM1555116 (H3.3, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1555116), GSM1207789 (Hira, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207789), GSM4774514 (Ezh2, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4774514), GSM4774522 (Jarid2, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4774522), GSM3483858 (Suz12, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3483858), GSM3483878 (H2AK119ub1, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3483878) and GSM3483853 (Ring1B, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3483853). Several ESC marker TF peak location files according published ChIP-seq data were downloaded from ENCODE (https://www.encodeproject.org/) under accession number ENCSR392DGA (Pou5f1 of ESCs, https://www.encodeproject.org/experiments/ENCSR392DGA/). The published E14TG2a datasets were downloaded from GEO under accession number GSE66582 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66582). Primers for genotyping and qPCR can be found in Supplementary Table 1. Summary of mouse genotypes can be found in Supplementary Tables 2–7. The gRNA and donor sequences for the CRISPR–Cas9 can be found in Supplementary Table 8. The antibody information used for CUT&Tag, scCUT&Tag, eSPAN, CUT&RUN, immunofluorescence, fluorescent activated cell sorting and western blot can be found in Supplementary Table 9.

Code availability

We have made use of publicly available software, tools and code. The public pipeline used to calculate bias via eSPAN analysis is available with the following link: https://github.com/clouds-drift/eSPAN-bias. The published scripts used to call lineage barcodes are available with the following link: https://github.com/AllonKleinLab/LARRY. All other codes used to generate the analysis in this study have been placed in Zenodo through the following link: https://doi.org/10.5281/zenodo.7866527.

References

  1. Stillman, B. Histone modifications: insights into their influence on gene expression. Cell 175, 6–9 (2018).

    Article  CAS  PubMed  Google Scholar 

  2. Bannister, A. J. & Kouzarides, T. Regulation of chromatin by histone modifications. Cell Res. 21, 381–395 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Scharf, A. N. et al. Monomethylation of lysine 20 on histone H4 facilitates chromatin maturation. Mol. Cell. Biol. 29, 57–67 (2009).

    Article  CAS  PubMed  Google Scholar 

  4. Alabert, C. et al. Two distinct modes for propagation of histone PTMs across the cell cycle. Genes Dev. 29, 585–590 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Xu, M., Wang, W., Chen, S. & Zhu, B. A model for mitotic inheritance of histone lysine methylation. EMBO Rep. 13, 60–67 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Stewart-Morgan, K. R., Petryk, N. & Groth, A. Chromatin replication and epigenetic cell memory. Nat. Cell Biol. 22, 361–371 (2020).

    Article  CAS  PubMed  Google Scholar 

  7. Gan, H. et al. The Mcm2-Ctf4-Polalpha axis facilitates parental histone H3-H4 transfer to lagging strands. Mol. Cell 72, 140–151.e3 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Petryk, N. et al. MCM2 promotes symmetric inheritance of modified histones during DNA replication. Science 361, 1389–1392 (2018).

    Article  CAS  PubMed  Google Scholar 

  9. Yu, C. et al. A mechanism for preventing asymmetric histone segregation onto replicating DNA strands. Science 361, 1386–1389 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Reverón-Gómez, N. et al. Accurate recycling of parental histones reproduces the histone modification landscape during DNA replication. Mol. Cell 72, 239–249.e5 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Escobar, T. M. et al. Active and repressed chromatin domains exhibit distinct nucleosome segregation during DNA replication. Cell 179, 953–963.e11 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Schlissel, G. & Rine, J. The nucleosome core particle remembers its position through DNA replication and RNA transcription. Proc. Natl Acad. Sci. USA 116, 20605–20611 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Reinberg, D. & Vales, L. D. Chromatin domains rich in inheritance. Science 361, 33–34 (2018).

    Article  CAS  PubMed  Google Scholar 

  14. Li, Z. et al. DNA polymerase alpha interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands. Sci. Adv. 6, eabb5820 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Schuettengruber, B., Bourbon, H.-M., Di Croce, L. & Cavalli, G. Genome regulation by polycomb and trithorax: 70 years and counting. Cell 171, 34–57 (2017).

    Article  CAS  PubMed  Google Scholar 

  17. Morgan, M. A. J. & Shilatifard, A. Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation. Nat. Genet. 52, 1271–1281 (2020).

    Article  CAS  PubMed  Google Scholar 

  18. Yu, C. et al. Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall. Mol. Cell 56, 551–563 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Li, S., Prasanna, X., Salo, V. T., Vattulainen, I. & Ikonen, E. An efficient auxin-inducible degron system with low basal degradation in human cells. Nat. Methods 16, 866–869 (2019).

    Article  CAS  PubMed  Google Scholar 

  20. Ming, X. et al. Kinetics and mechanisms of mitotic inheritance of DNA methylation and their roles in aging-associated methylome deterioration. Cell Res. 30, 980–996 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Weinreb, C., Rodriguez-Fraticelli, A., Camargo, F. D. & Klein, A. M. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science 367, eaaw3381 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Bartosovic, M., Kabbe, M. & Castelo-Branco, G. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues. Nat. Biotechnol. 39, 825–835 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Wu, S. J. et al. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nat. Biotechnol. 39, 819–824 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Afsari, B., Geman, D. & Fertig, E. J. Learning dysregulated pathways in cancers from differential variability analysis. Cancer Inform. 13, 61–67 (2014).

    PubMed  PubMed Central  Google Scholar 

  25. Ramachandran, S. & Henikoff, S. Transcriptional regulators compete with nucleosomes post-replication. Cell 165, 580–592 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Stewart-Morgan, K. R., Reveron-Gomez, N. & Groth, A. Transcription restart establishes chromatin accessibility after DNA replication. Mol. Cell 75, 284–297.e6 (2019).

    Article  CAS  PubMed  Google Scholar 

  27. Banaszynski, L. A. et al. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 155, 107–120 (2013).

    Article  CAS  PubMed  Google Scholar 

  28. Zhang, H. et al. RPA interacts with HIRA and regulates H3.3 deposition at gene regulatory elements in mammalian cells. Mol. Cell 65, 272–284 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Goldberg, A. D. et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140, 678–691 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Xu, X. et al. Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions. Nat. Commun. 13, 2514 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Hojfeldt, J. W. et al. Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. Nat. Struct. Mol. Biol. 25, 225–232 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Xie, J. et al. Histone H3 threonine phosphorylation regulates asymmetric histone inheritance in the Drosophila male germline. Cell 163, 920–933 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Wooten, M. et al. Asymmetric histone inheritance via strand-specific incorporation and biased replication fork movement. Nat. Struct. Mol. Biol. 26, 732–743 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Tran, V., Lim, C., Xie, J. & Chen, X. Asymmetric division of Drosophila male germline stem cell shows asymmetric histone distribution. Science 338, 679–682 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Saxton, D. S. & Rine, J. Epigenetic memory independent of symmetric histone inheritance. eLife 8, e51421 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Xu, X., Hua, X., Brown, K., Ren, X. & Zhang, Z. Mcm2 promotes stem cell differentiation via its ability to bind H3-H4. eLife 11, e80917 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  37. Atlasi, Y. & Stunnenberg, H. G. The interplay of epigenetic marks during stem cell differentiation and development. Nat. Rev. Genet. 18, 643–658 (2017).

    Article  CAS  PubMed  Google Scholar 

  38. Wu, J. et al. Stem cells and interspecies chimaeras. Nature 540, 51–59 (2016).

    Article  CAS  PubMed  Google Scholar 

  39. Ran, F. A. et al. Genome engineering using the CRISPR–Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Conti, L. et al. Niche-independent symmetrical self-renewal of a mammalian tissue stem cell. PLoS Biol. 3, e283 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Carter, B. et al. Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq). Nat. Commun. 10, 3747 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  42. Li, Z., Hua, X., Serra-Cardona, A., Xu, X. & Zhang, Z. Efficient and strand-specific profiling of replicating chromatin with enrichment and sequencing of protein-associated nascent DNA in mammalian cells. Nat. Protoc. 16, 2698–2721 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Q. Li (Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences) for his suggestions and help with embryonic staining, and K. Harper of Harper Health & Science Communications, LLC, for editorial assistance. This work was supported by the following funding: National Key R&D Program of China (grant no. 2019YFA0903800 to H.G.), the Major Program of the National Natural Science Foundation of China (32090031 to H.G.), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB0480000 to H.G.), the General Program of the National Natural Science Foundation of China (32070610 to H.G.), the National Natural Science Foundation of China for Young Scholars (32000580 to Q.W., 32001043 to Y.S., 32100460 to J.Z. and 32101178 to Y.Y.), the Guangdong Province Fund for Distinguished Young Scholars (2021B1515020109 to H.G.), Guangdong Basic and Applied Basic Research Foundation (2021A1515110377 to X.K.), Shenzhen Institute of Synthetic Biology Scientific Research Program (JCHZ20200005, ZTXM20190019 to H.G.) and National Institutes of Health Grant (R01GM130588 to C.Y.).

Author information

Author notes

  1. These authors contributed equally: Qing Wen, Jiaqi Zhou, Congcong Tian, Xinran Li, Guibing Song.

Authors and Affiliations

  1. CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China

    Qing Wen, Jiaqi Zhou, Congcong Tian, Xinran Li, Guibing Song, Yaping Sun, Sitong Yao, Xiaoyan Liang, Xing Kang, Nan Wang, Yuan Yao & Haiyun Gan

  2. College of Animal Science and Technology, Northwest A&F University, Yangling, China

    Guibing Song & Hongbao Wang

  3. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Yuan Gao

  4. Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China

    Chiyuan Ma & Xiaohua Lei

  5. College of Veterinary Medicine, South China Agricultural University, Guangzhou, China

    Sitong Yao & Xiaohuan Liang

  6. Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China

    Jialin Tang & Xiangyu Liu

  7. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA

    Steven M. Offer

  8. Hormel Institute, University of Minnesota, Austin, MN, USA

    Chuanhe Yu

  9. Department of Hematology, The Second People’s Hospital of Shenzhen, Shenzhen, China

    Xiangyu Liu

  10. School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China

    Zichuan Liu

  11. Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China

    Zichuan Liu

  12. Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA

    Zhiquan Wang

Authors
  1. Qing Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiaqi Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Congcong Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xinran Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Guibing Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yuan Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yaping Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Chiyuan Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Sitong Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Xiaoyan Liang
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Xing Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Nan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Yuan Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Hongbao Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Xiaohuan Liang
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Jialin Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Steven M. Offer
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Xiaohua Lei
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Chuanhe Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Xiangyu Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Zichuan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Zhiquan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Haiyun Gan
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

H.G. supervised the research. H.G. and Q.W. conceived and designed the experiments. Q.W., C.T., G.S., Y.S., C.M., S.Y., Xiaoyan Liang and X. Lei performed the experiments. H.G., Q.W., J.Z., C.T., X. Li, G.S., C.M., S.Y., Xiaoyan Liang and X. Lei performed statistical analysis. H.G., Q.W., J.Z., C.T., X.L., G.S., Y.G., C.M., S.Y., Xiaoyan Liang, X. Lei., Z.L. and Z.W. analyzed the data. H.G., Q.W., J.Z., Y.S., X.K., N.W., Y.Y., H.W., Xiaohuan Liang, J.T., S.M.O., X. Lei, X. Liu and Z.L. contributed materials. H.G., Q.W., Y.G., S.M.O., C.Y., X. Liu, Z.L. and Z.W. wrote the paper.

Corresponding author

Correspondence to Haiyun Gan.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Genetics thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–28 (unprocessed immunoblots), Tables 1–9, Notes 1–11 and references.

Reporting Summary

Peer Review File

Supplementary Data

Exact P values of Supplementary Figs. 2d (H3K27me3, H3K4me3 and H3K9me3); 6a,b; 12a–e,i and 23a.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wen, Q., Zhou, J., Tian, C. et al. Symmetric inheritance of parental histones contributes to safeguarding the fate of mouse embryonic stem cells during differentiation. Nat Genet 55, 1555–1566 (2023). https://doi.org/10.1038/s41588-023-01477-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41588-023-01477-w

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing