Abstract
Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases—namely, the chromatin remodellers1. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components2,3,4,5. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation6,7,8,9,10,11. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP–BeFx-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP–BeFx-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.
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Data availability
The structures have been deposited in the Protein Data Bank under accession codes 8WH8, 8WH9, 8WHA, 8WHB and 8WH5. The cryo-EM maps have been deposited in the Electron Microscopy Data Bank under accession codes EMD-37533, EMD-37535, EMD-37537, EMD-37538 and EMD-37529. Source data are provided with this paper.
References
Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273–304 (2009).
Shang, J. Y. & He, X. J. Chromatin-remodeling complexes: conserved and plant-specific subunits in Arabidopsis. J. Integr. Plant Biol. 64, 499–515 (2022).
Bieluszewski, T., Prakash, S., Roule, T. & Wagner, D. The role and activity of SWI/SNF chromatin remodelers. Annu. Rev. Plant Biol. 74, 139–163 (2023).
Guo, J. et al. Comprehensive characterization of three classes of Arabidopsis SWI/SNF chromatin remodelling complexes. Nat. Plants 8, 1423–1439 (2022).
Fu, W. et al. Organization, genomic targeting, and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis. Plant Cell 35, 2464–2483 (2023).
Jeddeloh, J. A., Stokes, T. L. & Richards, E. J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 22, 94–97 (1999).
Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926–1928 (1993).
Zhong, Z. et al. DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis. Proc. Natl Acad. Sci. USA 118, e2023347118 (2021).
Choi, S. H. et al. Mutation in DDM1 inhibits the homology directed repair of double strand breaks. PLoS ONE 14, e0211878 (2019).
Miura, A. et al. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411, 212–214 (2001).
Akinmusola, R. Y., Wilkins, C. A. & Doughty, J. DDM1-mediated TE silencing in plants. Plants (Basel) 12, 437 (2023).
Zhang, H., Lang, Z. & Zhu, J. K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489–506 (2018).
Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).
Goll, M. G. & Bestor, T. H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74, 481–514 (2005).
Du, J., Johnson, L. M., Jacobsen, S. E. & Patel, D. J. DNA methylation pathways and their crosstalk with histone methylation. Nat. Rev. Mol. Cell Biol. 16, 519–532 (2015).
Kanno, T. et al. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr. Biol. 14, 801–805 (2004).
Kanno, T. et al. A SNF2-like protein facilitates dynamic control of DNA methylation. EMBO Rep. 6, 649–655 (2005).
Zemach, A. et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193–205 (2013).
Brzeski, J. & Jerzmanowski, A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278, 823–828 (2003).
Osakabe, A. et al. The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W. Nat. Cell Biol. 23, 391–400 (2021).
Jamge, B. et al. Histone variants shape chromatin states in Arabidopsis. eLife 12, RP87714 (2023).
Zhou, J. et al. DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis. Sci. Adv. 9, eadg2699 (2023).
Li, M. et al. Mechanism of DNA translocation underlying chromatin remodelling by Snf2. Nature 567, 409–413 (2019).
Liu, X., Li, M., Xia, X., Li, X. & Chen, Z. Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure. Nature 544, 440–445 (2017).
Chabre, M. Aluminofluoride and beryllofluoride complexes: new phosphate analogs in enzymology. Trends Biochem. Sci. 15, 6–10 (1990).
Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251–260 (1997).
Lee, S. C. et al. Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Cell 186, 4100–4116 e15 (2023).
Osakabe, A. et al. Molecular and structural basis of the heterochromatin-specific chromatin remodeling activity by Arabidopsis DDM1. Preprint at bioRxiv https://doi.org/10.1101/2023.07.10.548306 (2023).
Paintsil, E. A. & Morrison, E. A. Preparation of recombinant histones and Widom 601 DNA for reconstitution of nucleosome core particles. Methods Mol. Biol. 2599, 163–175 (2023).
Hammonds, E. F. & Morrison, E. A. Nucleosome core particle reconstitution with recombinant histones and Widom 601 DNA. Methods Mol. Biol. 2599, 177–190 (2023).
Stark, H. GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM. Methods Enzymol. 481, 109–126 (2010).
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Zivanov, J., Nakane, T. & Scheres, S. H. W. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCrJ 7, 253–267 (2020).
Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012).
Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D Struct. Biol. 74, 531–544 (2018).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Kiianitsa, K., Solinger, J. A. & Heyer, W. D. NADH-coupled microplate photometric assay for kinetic studies of ATP-hydrolyzing enzymes with low and high specific activities. Anal. Biochem. 321, 266–271 (2003).
Acknowledgements
We thank H. Huang for discussion, the staff at SUSTech Cryo-EM Center for help in data collection and SUSTech Core Research Facilities for help with the circular dichroism experiment. This work was supported by the National Natural Science Foundation of China (grant no. 32325008 to J.D.), the Shenzhen Science and Technology Program (grant nos RCJC20221008092720004, KQTD20190929173906742 and 20231120201445001 to J.D.) and the EMBO Postdoctoral Fellowship (ALTF 579-2022 to H.H.).
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Y.L. and Z.Z. performed the experiments. F.Z., Q.W., C.W., H.H., W.C. and K.Y. contributed to the data collection, structural determination, analysis and discussion. J.D. conceived the study and wrote the paper.
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Extended data
Extended Data Fig. 1 ATPase activity assay and Circular Dichroism (CD) spectroscopy.
a. Principle of ATPase activity assay. b. The ATPase activity of DDM1, data are mean ± SD (n = 3 independent experiments), two-tailed Student’s t-test was applied, *** indicates P-value < 0.001. Green dots represent individual data points. The P values are: no NCP, 6.3 × 10−8; no DDM1, 1.1 × 10−7; no DDM1/NCP, 4.6 × 10−7; no DDM1/NCP/ATP, 1.8 × 10−8. c. The SDS-PAGE of purified AtDDM1-ΔN25 (ΔN) and full-length protein (FL) stained by Coomassie brilliant blue. The proteins were purified more than 3 times with similar result. d. The ATPase activity of DDM1 FL and ΔN. Data are mean ± SD (n = 3 independent experiments), two-tailed Student’s t-test was applied with P-value of 0.14 which is greater than 0.05, suggesting no statistical significance (ns) between the two datasets. Green dots represent individual data points. e. CD spectra of AtDDM1-ΔN25, full-length (FL), and the mutants at wavelength 200–240 nm. All the proteins possess similar CD patterns, suggesting a well-folded state with similar secondary structure components.
Extended Data Fig. 2 Cryo-EM structure analysis of the DDM1-NCP complex in ADP-bound state.
a. The SDS-PAGE of purified AtDDM1-ΔN25 stained with Coomassie brilliant blue. The protein was purified more than 3 times with similar result. b. Flow chart of cryo-EM data processing. c. Representative micrograph of cryo-EM sample. Scale bar: 50 nm. d. Representative 2D class averages. e. Local resolution map. f. The gold-standard FSC curves calculated between two halves of datasets. g. Angular distribution of particle projections of ADP-complex.
Extended Data Fig. 3 Cryo-EM maps for representative regions of DDM1-NCP complex in ADP bound form.
a-h. Electron density maps showed the fitting of ADP (a) and representative protein regions (b-h).
Extended Data Fig. 4 Comparison of the structures of the DDM1-NCP complex and ScSnf2-NCP complex.
a. Superimposition of the structures of the DDM1-NCP complex (color-coded) and ScSnf2-NCP complex (gray, PDB code: 5Z3O). b. Comparison of the structures of the H4 tail binding pockets in DDM1-NCP complex and the ScSnf2-NCP complex (gray, PDB code: 5X0Y). Acidic residues of structures surrounding the H4-binding pocket are shown as sticks and labelled, respectively.
Extended Data Fig. 5 Cryo-EM structure analysis of the DDM1-NCP complex in nucleotide-free state.
a. Flow chart of cryo-EM data processing. b. Representative micrograph of cryo-EM sample. Scale bar: 50 nm. c. Representative 2D class averages. d. Local resolution map. e. The gold-standard FSC curves calculated between two halves of datasets. f. Angular distribution of particle projections of the DDM1-nucleosome complex.
Extended Data Fig. 6 Cryo-EM structure analysis of the DDM1-NCP complex in ADP-BeFx-complexed states.
a. Flow chart of cryo-EM data processing. b. Representative micrograph of cryo-EM sample. Scale bar: 50 nm. c. Representative 2D class averages. d. The gold-standard FSC curves calculated between two halves of datasets.
Extended Data Fig. 7 Cryo-EM maps.
a-s. Electron density maps showed the fitting of representative regions of DDM1-NCP complex in nucleotide-free form (a-g), ADP-BeFx-bound conformation (h-o), and free Arabidopsis NCP (p-s).
Extended Data Fig. 8 Cryo-EM structure of DDM1-NCP complex in ADP-BeFx-bound state and free Arabidopsis NCP.
a. The 2DDM1-1NCP complex in ADP-BeFx-bound state with DDM1 bound to SHL2 and SHL-2. b-c. The superimpositions of the 1:1 complex (in silver) to the DDM1 at SHL2 (b) and SHL-2 (c) positions in the 2:1 complex showing very similar overall structures and NCP binding mode. d. Superimposition of the structures of the Arabidopsis NCP (in color) and the Xenopus laevis NCP (in silver, PDB code: 1AOI). The overall superimposition RMSD is only 0.56 Å.
Extended Data Fig. 9 Proposed mechanism for the directional translocation of DNA by DDM1 upon ATP binding and hydrolysis at the DDM1-NCP interface.
a. Superimposition of the structures of DDM1-NCP in nucleotide-free (color-coded) and ADP-BeFx-bound (gray) states aligned by the histone octamers. The boxed regions are enlarged for further analysis in panels b-c. b. DDM1 Lobe2-DNA interface in the purple boxed region in panel a. The directions of Lobe2 movement and DNA sliding upon ATP binding are highlighted by black and red arrows, respectively. c. Lobe1-DNA interface in the orange boxed region in panel a. d. Superimposition of the structures of DDM1-NCP in ADP-BeFx-bound (color-coded) and ADP-bound (gray) states aligned by the histone octamers. The boxed region is enlarged for further analysis in panel e. e. DDM1-DNA interface in the boxed region in panel d.
Extended Data Fig. 10 Structural comparison of DDM1-H3.1 NCP complex and DDM1-H3.3/H2A.W NCP complex (PDB code: 7UX9).
a. Superimpositions of the DDM1-NCP complexes in the nucleotide-free, ADP-BeFx-bound, and ADP-bound states, and the DDM1-H3.3/H2A.W NCP complex. The histone octamers are aligned. b. Comparison of the detailed interactions of DDM1 with histone H3.1 in ADP-bound state in this study (color-coded) and H3.3 in the H3.3/H2A.W NCP complex (gray) state. The boxed region is enlarged for further analysis in right panel, the interacting residues are shown as sticks and labelled, respectively. c. A view of residues C615 and C634 in the Lobe2 domain of DDM1 in our study. The boxed region is enlarged for further analysis in right panel, the residues are shown as sticks, cryo-EM density is shown as a gray volume.
Supplementary information
Supplementary Information
Supplementary Tables 1 and 2.
Supplementary Video 1
Video showing the coupling of DNA movement with the domain motion of DDM1 in a chromatin remodelling cycle.
Source data
Source Data Fig. 2
Original data for Fig. 2g.
Source Data Extended Data Fig. 1
Original data for Extended Data Fig. 1b,d and unmodified gel for Extended Data Fig. 1c.
Source Data Extended Data Fig. 2
Unmodified gel for Extended Data Fig. 2a.
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Liu, Y., Zhang, Z., Hu, H. et al. Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. Nat. Plants 10, 374–380 (2024). https://doi.org/10.1038/s41477-024-01640-z
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DOI: https://doi.org/10.1038/s41477-024-01640-z
