Abstract
DNMT1 is a DNA methyltransferase that catalyzes and maintains methylation in CpG dinucleotides. It blocks the entrance of DNA into the catalytic pocket via the replication foci targeting sequence (RFTS) domain. Recent studies have shown that an H3-tail-conjugated two-mono-ubiquitin mark (H3Ub2) activates DNMT1 by binding to the RFTS domain. However, the activation mechanism of DNMT1 remains unclear. In this work, we combine various sampling methods of extensive simulations, including conventional molecular dynamics, Gaussian-accelerated molecular dynamics, and coarse-grained molecular dynamics, to elucidate the activation mechanism of DNMT1. Geometric and energy analyses show that binding of H3Ub2 to the RFTS domain of DNMT1 results in the bending of the α4-helix in the RFTS domain at approximately 30°–35°, and the RFTS domain rotates ∼20° anti-clockwise and moves ∼3 Å away from the target recognition domain (TRD). The hydrogen-bonding network at the RFTS-TRD interface is significantly disrupted, implying that the RFTS domain is dissociated from the catalytic core, which contributes to activating the auto-inhibited conformation of DNMT1. These results provide structural and dynamic evidence for the role of H3Ub2 in regulating the catalytic activity of DNMT1.
Similar content being viewed by others
References
Bachman, K.E., Park, B.H., Rhee, I., Rajagopalan, H., Herman, J.G., Baylin, S.B., Kinzler, K.W., and Vogelstein, B. (2003). Histone modifications and silencing prior to DNA methylation of a tumor suppressor gene. Cancer Cell 3, 89–95.
Bostick, M., Kim, J.K., Esteve, P.O., Clark, A., Pradhan, S., and Jacobsen, S.E. (2007). UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317, 1760–1764.
Bueren-Calabuig, J.A., G. Bage, M., Cowling, V.H., and Pisliakov, A.V. (2019). Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: insights from accelerated molecular dynamics simulations. Nucl Acids Res 47, 8675–8692.
Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B., and Woods, R.J. (2005). The Amber biomolecular simulation programs. J Comput Chem 26, 1668–1688.
Cheng, J., Yang, H., Fang, J., Ma, L., Gong, R., Wang, P., et al. (2015). Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation. The 14th China International Biophysics Conference. Heidelberg: Springer. 7023.
Chong, L.T., Duan, Y., Wang, L., Massova, I., and Kollman, P.A. (1999). Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc Natl Acad Sci USA 96, 14330–14335.
Eargle, J., and Luthey-Schulten, Z. (2012). NetworkView: 3D display and analysis of protein·RNA interaction networks. Bioinformatics 28, 3000–3001.
Girvan, M., and Newman, M.E.J. (2002). Community structure in social and biological networks. Proc Natl Acad Sci USA 99, 7821–7826.
Guo, X., Wang, L., Li, J., Ding, Z., Xiao, J., Yin, X., He, S., Shi, P., Dong, L., Li, G., et al. (2015). Structural insight into autoinhibition and histone H3-induced activation of DNMT3A. Nature 517, 640–644.
Helming, K.C., Wang, X., and Roberts, C.W.M. (2014). Vulnerabilities of mutant SWI/SNF complexes in cancer. Cancer Cell 26, 309–317.
Illingworth, R.S., and Bird, A.P. (2009). CpG islands—“a rough guide”. FEBS Lett 583, 1713–1720.
Ishiyama, S., Nishiyama, A., Saeki, Y., Moritsugu, K., Morimoto, D., Yamaguchi, L., Arai, N., Matsumura, R., Kawakami, T., Mishima, Y., et al. (2017). Structure of the Dnmt1 reader module complexed with a unique two-mono-ubiquitin mark on histone H3 reveals the basis for DNA methylation maintenance. Mol Cell 68, 350–360.e7.
Jones, P.A., and Takai, D. (2001). The role of DNA methylation in mammalian epigenetics. Science 293, 1068–1070.
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., and Klein, M.L. (1983). Comparison of simple potential functions for simulating liquid water. J Chem Phys 79, 926–935.
Kanada, K., Takeshita, K., Suetake, I., Tajima, S., and Nakagawa, A. (2017). Conserved threonine 1505 in the catalytic domain stabilizes mouse DNA methyltransferase 1. J Biochem, doi: https://doi.org/10.1093/jb/mvx024.
Kelly, T.K., De Carvalho, D.D., and Jones, P.A. (2010). Epigenetic modifications as therapeutic targets. Nat Biotechnol 28, 1069–1078.
Kollman, P.A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., et al. (2000). Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33, 889–897.
Li, T., Wang, L., Du, Y., Xie, S., Yang, X., Lian, F., Zhou, Z., and Qian, C. (2018). Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation. Nucl Acids Res 46, 3218–3231.
Li, W., and Mills, A.A. (2014). Architects of the genome: CHD dysfunction in cancer, developmental disorders and neurological syndromes. Epigenomics 6, 381–395.
Liang, Z., Zhu, Y., Long, J., Ye, F., and Hu, G. (2020). Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s. Comput Struct Biotechnol J 18, 749–764.
Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., and Simmerling, C. (2015). ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theor Comput 11, 3696–3713.
Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., and de Vries, A. H. (2007). The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111, 7812–7824.
Miao, Y., Feher, V.A., and McCammon, J.A. (2015). Gaussian accelerated molecular dynamics: unconstrained enhanced sampling and free energy calculation. J Chem Theor Comput 11, 3584–3595.
Miao, Y., Sinko, W., Pierce, L., Bucher, D., Walker, R.C., and McCammon, J.A. (2014). Improved reweighting of accelerated molecular dynamics simulations for free energy calculation. J Chem Theor Comput 10, 2677–2689.
Nishiyama, A., Yamaguchi, L., Sharif, J., Johmura, Y., Kawamura, T., Nakanishi, K., Shimamura, S., Arita, K., Kodama, T., Ishikawa, F., et al. (2013). Uhrf1-dependent H3K23 ubiquitylation couples maintenance DNA methylation and replication. Nature 502, 249–253.
Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M.R., Smith, J.C., Kasson, P.M., van der Spoel, D., et al. (2013). GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854.
Qin, W., Wolf, P., Liu, N., Link, S., Smets, M., La Mastra, F., Forné, I., Pichler, G., Hörl, D., Fellinger, K., et al. (2015). DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination. Cell Res 25, 911–929.
Robertson, K.D., and Wolffe, A.P. (2000). DNA methylation in health and disease. Nat Rev Genet 1, 11–19.
Sethi, A., Eargle, J., Black, A.A., and Luthey-Schulten, Z. (2009). Dynamical networks in tRNA: protein complexes. Proc Natl Acad Sci USA 106, 6620–6625.
Sharif, J., Muto, M., Takebayashi, S.I., Suetake, I., Iwamatsu, A., Endo, T. A., Shinga, J., Mizutani-Koseki, Y., Toyoda, T., Okamura, K., et al. (2007). The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450, 908–912.
Song, J., Rechkoblit, O., Bestor, T.H., and Patel, D.J. (2011). Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331, 1036–1040.
Song, J., Teplova, M., Ishibe-Murakami, S., and Patel, D.J. (2012). Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science 335, 709–712.
Syeda, F., Fagan, R.L., Wean, M., Avvakumov, G.V., Walker, J.R., Xue, S., Dhe-Paganon, S., and Brenner, C. (2011). The replication focus targeting sequence (RFTS) domain is a DNA-competitive inhibitor of Dnmt1. J Biol Chem 286, 15344–15351.
Takeshita, K., Suetake, I., Yamashita, E., Suga, M., Narita, H., Nakagawa, A., and Tajima, S. (2011). Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1). Proc Natl Acad Sci USA 108, 9055–9059.
Ye, F., Kong, X., Zhang, H., Liu, Y., Shao, Z., Jin, J., Cai, Y., Zhang, R., Li, L., Zhang, Y.W., et al. (2018). Biochemical studies and molecular dynamic simulations reveal the molecular basis of conformational changes in DNA methyltransferase-1. ACS Chem Biol 13, 772–781.
Zhang, Z.M., Liu, S., Lin, K., Luo, Y., Perry, J.J., Wang, Y., and Song, J. (2015). Crystal structure of human DNA methyltransferase 1. J Mol Biol 427, 2520–2531.
Zhu, Y., Ye, F., Zhou, Z., Liu, W., Liang, Z., and Hu, G. (2021). Insights into conformational dynamics and allostery in DNMT1-H3Ub/USP7 interactions. Molecules 26, 5153.
Acknowledgements
This work was supported by the Chinese Ministry of Science and Technology and Natural Science Foundation of China (2019YFA0508902, 2018YFA0107004, 32170549, 31870737, 22103040), the National Laboratory of Biomacromolecules (2021kf05), the Fundamental Research Funds for the Central Universities and Tianjin Funds for Distinguished Young Scientists (17JCJQJC45900).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Compliance and ethics The author(s) declare that they have no conflict of interest.
Electronic supplementary material
11427_2021_2179_MOESM1_ESM.docx
Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination, revealed by multi-scale molecular dynamics simulations
Rights and permissions
About this article
Cite this article
Sun, J., Liu, F., Yuan, L. et al. Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination, revealed by multi-scale molecular dynamics simulations. Sci. China Life Sci. 66, 313–323 (2023). https://doi.org/10.1007/s11427-021-2179-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11427-021-2179-8