Tunable DNMT1 Degradation Reveals DNMT1/DNMT3B Synergy in DNA Methylation and Genome Organization

Overview

Journal J Cell Biol

Specialty Cell Biology

Date 2024 Feb 20

PMID 38376465

Authors

Andrea Scelfo

Viviana Barra

Nezar Abdennur

George Spracklin

Florence Busato

Catalina Salinas-Luypaert

Elena Bonaiti

Guillaume Velasco

Frederic Bonhomme

Anna Chipont

Andrea E Tijhuis

Diana C J Spierings

Coralie Guerin

Paola Arimondo

Claire Francastel

Floris Foijer

Jrg Tost

Leonid Mirny

Daniele Fachinetti

Affiliations

Soon will be listed here.

Abstract

DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present cell models that allow inducible and reversible DNAme modulation through DNMT1 depletion. By dynamically assessing whole genome and locus-specific effects of induced passive demethylation through cell divisions, we reveal a cooperative activity between DNMT1 and DNMT3B, but not of DNMT3A, to maintain and control DNAme. We show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin, compartmentalization, and peripheral localization. DNA methylation loss coincides with a gradual reduction of cell fitness due to G1 arrest, with minor levels of mitotic failure. Altogether, this system allows DNMTs and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNAme dysfunction and human disease.

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References

Nishiyama A, Nakanishi M . Navigating the DNA methylation landscape of cancer. Trends Genet. 2021; 37(11):1012-1027. DOI: 10.1016/j.tig.2021.05.002. View

Jin B, Li Y, Robertson K . DNA methylation: superior or subordinate in the epigenetic hierarchy?. Genes Cancer. 2011; 2(6):607-17. PMC: 3174260. DOI: 10.1177/1947601910393957. View

Rokavec M, Horst D, Hermeking H . Cellular Model of Colon Cancer Progression Reveals Signatures of mRNAs, miRNA, lncRNAs, and Epigenetic Modifications Associated with Metastasis. Cancer Res. 2017; 77(8):1854-1867. DOI: 10.1158/0008-5472.CAN-16-3236. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Jair K, Bachman K, Suzuki H, Ting A, Rhee I, Yen R . De novo CpG island methylation in human cancer cells. Cancer Res. 2006; 66(2):682-92. DOI: 10.1158/0008-5472.CAN-05-1980. View

Hansen R, Wijmenga C, Luo P, Stanek A, Canfield T, Weemaes C . The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci U S A. 1999; 96(25):14412-7. PMC: 24450. DOI: 10.1073/pnas.96.25.14412. View

Xiong K, Ma J . Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. Nat Commun. 2019; 10(1):5069. PMC: 6838123. DOI: 10.1038/s41467-019-12954-4. View

Bakker B, Taudt A, Belderbos M, Porubsky D, Spierings D, de Jong T . Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. Genome Biol. 2016; 17(1):115. PMC: 4888588. DOI: 10.1186/s13059-016-0971-7. View

Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A . Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289-93. PMC: 2858594. DOI: 10.1126/science.1181369. View

10.

Juttermann R, Li E, Jaenisch R . Toxicity of 5-aza-2'-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation. Proc Natl Acad Sci U S A. 1994; 91(25):11797-801. PMC: 45322. DOI: 10.1073/pnas.91.25.11797. View

11.

Pappalardi M, Keenan K, Cockerill M, Kellner W, Stowell A, Sherk C . Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer. 2021; 2(10):1002-1017. PMC: 8594913. View

12.

Loonstra A, Vooijs M, Beverloo H, Allak B, van Drunen E, Kanaar R . Growth inhibition and DNA damage induced by Cre recombinase in mammalian cells. Proc Natl Acad Sci U S A. 2001; 98(16):9209-14. PMC: 55399. DOI: 10.1073/pnas.161269798. View

13.

Robertson K . DNA methylation and human disease. Nat Rev Genet. 2005; 6(8):597-610. DOI: 10.1038/nrg1655. View

14.

Du Q, Smith G, Luu P, Ferguson J, Armstrong N, Caldon C . DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity. Cell Rep. 2021; 36(12):109722. DOI: 10.1016/j.celrep.2021.109722. View

15.

Samanta S, Rajasingh S, Cao T, Dawn B, Rajasingh J . Epigenetic dysfunctional diseases and therapy for infection and inflammation. Biochim Biophys Acta Mol Basis Dis. 2016; 1863(2):518-528. PMC: 5222695. DOI: 10.1016/j.bbadis.2016.11.030. View

16.

Fu K, Bonora G, Pellegrini M . Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues. Epigenetics. 2019; 15(3):272-282. PMC: 7028327. DOI: 10.1080/15592294.2019.1666649. View

17.

Rao S, Huntley M, Durand N, Stamenova E, Bochkov I, Robinson J . A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159(7):1665-80. PMC: 5635824. DOI: 10.1016/j.cell.2014.11.021. View

18.

Vilkaitis G, Suetake I, Klimasauskas S, Tajima S . Processive methylation of hemimethylated CpG sites by mouse Dnmt1 DNA methyltransferase. J Biol Chem. 2004; 280(1):64-72. DOI: 10.1074/jbc.M411126200. View

19.

Rhee I, Bachman K, Park B, Jair K, Yen R, Schuebel K . DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature. 2002; 416(6880):552-6. DOI: 10.1038/416552a. View

20.

Scelfo A, Fernandez-Perez D, Tamburri S, Zanotti M, Lavarone E, Soldi M . Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities. Mol Cell. 2019; 74(5):1037-1052.e7. PMC: 6561742. DOI: 10.1016/j.molcel.2019.04.002. View