Kinetics and mechanisms of mitotic inheritance of DNA methylation and their roles in aging-associated methylome deterioration

Abstract

Mitotic inheritance of the DNA methylome is a challenging task for the maintenance of cell identity. Whether DNA methylation pattern in different genomic contexts can all be faithfully maintained is an open question. A replication-coupled DNA methylation maintenance model was proposed decades ago, but some observations suggest that a replication-uncoupled maintenance mechanism exists. However, the capacity and the underlying molecular events of replication-uncoupled maintenance are unclear. By measuring maintenance kinetics at the single-molecule level and assessing mutant cells with perturbation of various mechanisms, we found that the kinetics of replication-coupled maintenance are governed by the UHRF1–Ligase 1 and PCNA–DNMT1 interactions, whereas nucleosome occupancy and the interaction between UHRF1 and methylated H3K9 specifically regulate replication-uncoupled maintenance. Surprisingly, replication-uncoupled maintenance is sufficiently robust to largely restore the methylome when replication-coupled maintenance is severely impaired. However, solo-WCGW sites and other CpG sites displaying aging- and cancer-associated hypomethylation exhibit low maintenance efficiency, suggesting that although quite robust, mitotic inheritance of methylation is imperfect and that this imperfection may contribute to selective hypomethylation during aging and tumorigenesis.

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Fig. 1: Hammer-seq delineates the kinetics of methylation maintenance.
Fig. 2: The UHRF1–Ligase 1 and DNMT1–PCNA interactions contribute to rapid maintenance methylation in the DNA replication-coupled phase.
Fig. 3: Interaction between the UHRF1 tudor domain and H3K9me2 balances the intrinsic disadvantage of methylation maintenance in these regions.
Fig. 4: The replication-uncoupled phase has potent maintenance capacity.
Fig. 5: Nucleosome occupancy decelerates maintenance methylation kinetics in the replication-uncoupled phase.
Fig. 6: Solo-WCGW CpGs and other CpGs with preferential loss of methylation during aging display a low maintenance efficiency.
Fig. 7: The replication-uncoupled phase in late S replication domains shows a decreased maintenance rate and is highly dependent on LSH.

Data availability

HeLa OK-seq data were obtained from NCBI SRA under the accession number SRP065949.49 Histone H3 ChIP-seq of HeLa S3 was obtained from GSM788634.96 Aging associated DNA methylation change data was taken from pulication.68 All high throughput data generated in this study have been deposited at NCBI GEO under accession number: GSE131098. Custom scripts for data analysis used in this data are available upon reasonable requests.

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Acknowledgements

We thank J.Y. Jia and S. Sun for technical assistance in FACS analysis. This work was primarily supported by the National Natural Science Foundation of China (31530047). This work was also supported by the Ministry of Science and Technology of China (2016YFA0100400), the Chinese Academy of Sciences (XDB39000000 and QYZDY-SSW-SMC031). Z.Z. is sponsored by the Youth Innovation Promotion Association (2017133) of the Chinese Academy of Sciences.

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X.M., Z.Z. and B.Z. conceived and designed this project. X.M. performed the majority of experiments. Z.Z. performed bioinformatics analysis. Z.Zou., Q.H., Y.Y. helped in mutant cell line establishment. C.L. performed the UHPLC-MS/MS experiments under the supervision of H.W. Q.D. participated in experimental design and some experiments. Y.L. participated in data analysis. X.M., Z.Z. and B.Z. wrote the manuscript with comments and contributions from all authors.

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Correspondence to Bing Zhu.

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Ming, X., Zhang, Z., Zou, Z. et al. Kinetics and mechanisms of mitotic inheritance of DNA methylation and their roles in aging-associated methylome deterioration. Cell Res (2020). https://doi.org/10.1038/s41422-020-0359-9

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