The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.

Hannah Wapenaar; Gillian Clifford; Willow Rolls; Moira Pasquier; Hayden Burdett; Yujie  Zhang; Gauri Deák; Juan Zou; Christos Spanos; Mark R. D. Taylor; Jacquie Mills; James A. Watson; Dhananjay Kumar; Richard Clark; Alakta Das; Devisree Valsakumar; Janice Bramham; Philipp Voigt; Duncan Sproul; Marcus D. Wilson

doi:10.1038/s44319-024-00306-3

The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.

Hannah Wapenaar, Gillian Clifford, Willow Rolls, Moira Pasquier, Hayden Burdett, Yujie Zhang, Gauri Deák, Juan Zou, Christos Spanos, Mark R. D. Taylor, Jacquie Mills, James A. Watson, Dhananjay Kumar, Richard Clark, Alakta Das, Devisree Valsakumar, Janice Bramham, Philipp Voigt, Duncan Sproul, Marcus D. Wilson^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of DNMT3A1 with diverse modified nucleosomes indicative of different chromatin environments. A cryo-EM structure of the full-length DNMT3A1-DNMT3L complex with a H2AK119ub nucleosome reveals that the DNMT3A1 ubiquitin-dependent recruitment (UDR) motif interacts specifically with H2AK119ub and makes extensive contacts with the core nucleosome histone surface. This interaction facilitates robust DNMT3A1 binding to nucleosomes, and previously unexplained DNMT3A disease-associated mutations disrupt this interface. Furthermore, the UDR-nucleosome interaction synergises with other DNMT3A chromatin reading elements in the absence of histone ubiquitylation. H2AK119ub does not stimulate DNMT3A DNA methylation activity, as observed for the previously described H3K36me2 mark, which may explain low levels of DNA methylation on H2AK119ub marked facultative heterochromatin. This study highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome surface and increases our understanding of how DNMT3A1 chromatin recruitment occurs.

Original language	English
Number of pages	37
Journal	EMBO Reports
Early online date	11 Nov 2024
DOIs	https://doi.org/10.1038/s44319-024-00306-3
Publication status	E-pub ahead of print - 11 Nov 2024

Keywords / Materials (for Non-textual outputs)

Chromatin
Cryo-EM
DNA methyltransferase
Histone
Epigenetic

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10.1038/s44319-024-00306-3

wapenaar-et-al-2024-the-n-terminal-region-of-dnmt3a-engages-the-nucleosome-surface-to-aid-chromatin-recruitmentFinal published version, 8.69 MBLicence: Creative Commons: Attribution (CC-BY)

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Wapenaar, H., Clifford, G., Rolls, W., Pasquier, M., Burdett, H., Zhang, Y., Deák, G., Zou, J., Spanos, C., Taylor, M. R. D., Mills, J., Watson, J. A., Kumar, D., Clark, R., Das, A., Valsakumar, D., Bramham, J., Voigt, P., Sproul, D., & Wilson, M. D. (2024). The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment. EMBO Reports. Advance online publication. https://doi.org/10.1038/s44319-024-00306-3

@article{b404e39b581d4017b19858d7f2b23a50,

title = "The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.",

abstract = "DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of DNMT3A1 with diverse modified nucleosomes indicative of different chromatin environments. A cryo-EM structure of the full-length DNMT3A1-DNMT3L complex with a H2AK119ub nucleosome reveals that the DNMT3A1 ubiquitin-dependent recruitment (UDR) motif interacts specifically with H2AK119ub and makes extensive contacts with the core nucleosome histone surface. This interaction facilitates robust DNMT3A1 binding to nucleosomes, and previously unexplained DNMT3A disease-associated mutations disrupt this interface. Furthermore, the UDR-nucleosome interaction synergises with other DNMT3A chromatin reading elements in the absence of histone ubiquitylation. H2AK119ub does not stimulate DNMT3A DNA methylation activity, as observed for the previously described H3K36me2 mark, which may explain low levels of DNA methylation on H2AK119ub marked facultative heterochromatin. This study highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome surface and increases our understanding of how DNMT3A1 chromatin recruitment occurs. ",

keywords = "Chromatin, Cryo-EM, DNA methyltransferase, Histone, Epigenetic",

author = "Hannah Wapenaar and Gillian Clifford and Willow Rolls and Moira Pasquier and Hayden Burdett and Yujie Zhang and Gauri De{\'a}k and Juan Zou and Christos Spanos and Taylor, {Mark R. D.} and Jacquie Mills and Watson, {James A.} and Dhananjay Kumar and Richard Clark and Alakta Das and Devisree Valsakumar and Janice Bramham and Philipp Voigt and Duncan Sproul and Wilson, {Marcus D.}",

note = "We thank Duncan Sproul, Adrian Bird and members of the Wilson lab for helpful discussions and critical reading of the manuscript. MDW{\textquoteright}s work is supported by the Sir Henry Dale Fellowship form the Wellcome Trust [210493/Z/18/Z], Medical Research Council (T029471/1), Scottish high-field NMR centre seed funding and University of Edinburgh. HW work is part supported by Institutional Strategic Support Fund (IS3-R1.37 22-23). Work in the Voigt lab was supported by the Wellcome Trust ([104175/Z/14/Z], Sir Henry Dale Fellowship to P.V.) and the UK Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0421). Work in the DS laboratory is supported by an MRC university grant to the MRC Human Genetics Unit. D.V, A.D, & D.K are supported by PhD studentships from the Darwin Trust of Edinburgh. W.R and J.A.W are funded by the Wellcome trust integrative cellular mechanisms PhD program (218470). M.P is supported by the MRC Human Genetics Unit PhD program. GD{\textquoteright}s work is supported by BBSRC EASTBIO [BB/M010996/1]. This work was supported by the Edinburgh Protein Production Facility (EPPF), which receives funding from a core grant (203149) to the Wellcome Centre for Cell Biology at the University of Edinburgh. Grid screening was performed in the cryo-EM facility in School of Biological Sciences at the University of Edinburgh, we are grateful to Maarten Tuijtel and Martin Singleton for their support. The cryo-EM facility was set up with funding from the Wellcome Trust (087658/Z/08/Z) and SULSA. We are grateful to the Rappsilber lab for access to the Xi server for mapping protein crosslinks. We thank Arthur Riggs, Joe Landry (via Addgene) Duncan Sproul and Frank Sicheri for gifts of plasmids. We are very grateful to David Owen, Julika Radecke and Matt Byrne at Diamond for access and support of the Cryo-EM facilities at the UK national electron bio-imaging centre (eBIC), proposal EM-BI24557 & EM-BI31827, funded by the Wellcome Trust, MRC and BBSRC. We are grateful to the Edinburgh Clinical Research Facility Genetics Core and Martin Taylor for insights to nanopore sequencing. This work was supported by the Wellcome Centre for Cell Biology Mass spectrometry facility which receives funding from a core grant to the Wellcome Centre for Cell Biology (203149) and a Multi-User Equipment grant(s) (108504). This work was supported by funding for the Wellcome Discovery Research Platform for Hidden Cell Biology [226791] and we gratefully acknowledge support from the Proteomics and Structural Biology cores. We thank Logan Mackay in SIRCAMS school of chemistry, university of Edinburgh for mass spec analysis. We thank Juraj Bella in the NMR facility, School of Chemistry, University of Edinburgh for help with NMR experiments. ",

year = "2024",

month = nov,

day = "11",

doi = "10.1038/s44319-024-00306-3",

language = "English",

journal = "EMBO Reports",

issn = "1469-221X",

publisher = "Wiley",

}

Wapenaar, H , Clifford, G, Rolls, W, Pasquier, M, Burdett, H, Zhang, Y, Deák, G, Zou, J, Spanos, C, Taylor, MRD, Mills, J, Watson, JA, Kumar, D, Clark, R, Das, A, Valsakumar, D, Bramham, J, Voigt, P, Sproul, D & Wilson, MD 2024, 'The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.', EMBO Reports. https://doi.org/10.1038/s44319-024-00306-3

TY - JOUR

T1 - The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.

AU - Wapenaar, Hannah

AU - Clifford, Gillian

AU - Rolls, Willow

AU - Pasquier, Moira

AU - Burdett, Hayden

AU - Zhang, Yujie

AU - Deák, Gauri

AU - Zou, Juan

AU - Spanos, Christos

AU - Taylor, Mark R. D.

AU - Mills, Jacquie

AU - Watson, James A.

AU - Kumar, Dhananjay

AU - Clark, Richard

AU - Das, Alakta

AU - Valsakumar, Devisree

AU - Bramham, Janice

AU - Voigt, Philipp

AU - Sproul, Duncan

AU - Wilson, Marcus D.

N1 - We thank Duncan Sproul, Adrian Bird and members of the Wilson lab for helpful discussions and critical reading of the manuscript. MDW’s work is supported by the Sir Henry Dale Fellowship form the Wellcome Trust [210493/Z/18/Z], Medical Research Council (T029471/1), Scottish high-field NMR centre seed funding and University of Edinburgh. HW work is part supported by Institutional Strategic Support Fund (IS3-R1.37 22-23). Work in the Voigt lab was supported by the Wellcome Trust ([104175/Z/14/Z], Sir Henry Dale Fellowship to P.V.) and the UK Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0421). Work in the DS laboratory is supported by an MRC university grant to the MRC Human Genetics Unit. D.V, A.D, & D.K are supported by PhD studentships from the Darwin Trust of Edinburgh. W.R and J.A.W are funded by the Wellcome trust integrative cellular mechanisms PhD program (218470). M.P is supported by the MRC Human Genetics Unit PhD program. GD’s work is supported by BBSRC EASTBIO [BB/M010996/1]. This work was supported by the Edinburgh Protein Production Facility (EPPF), which receives funding from a core grant (203149) to the Wellcome Centre for Cell Biology at the University of Edinburgh. Grid screening was performed in the cryo-EM facility in School of Biological Sciences at the University of Edinburgh, we are grateful to Maarten Tuijtel and Martin Singleton for their support. The cryo-EM facility was set up with funding from the Wellcome Trust (087658/Z/08/Z) and SULSA. We are grateful to the Rappsilber lab for access to the Xi server for mapping protein crosslinks. We thank Arthur Riggs, Joe Landry (via Addgene) Duncan Sproul and Frank Sicheri for gifts of plasmids. We are very grateful to David Owen, Julika Radecke and Matt Byrne at Diamond for access and support of the Cryo-EM facilities at the UK national electron bio-imaging centre (eBIC), proposal EM-BI24557 & EM-BI31827, funded by the Wellcome Trust, MRC and BBSRC. We are grateful to the Edinburgh Clinical Research Facility Genetics Core and Martin Taylor for insights to nanopore sequencing. This work was supported by the Wellcome Centre for Cell Biology Mass spectrometry facility which receives funding from a core grant to the Wellcome Centre for Cell Biology (203149) and a Multi-User Equipment grant(s) (108504). This work was supported by funding for the Wellcome Discovery Research Platform for Hidden Cell Biology [226791] and we gratefully acknowledge support from the Proteomics and Structural Biology cores. We thank Logan Mackay in SIRCAMS school of chemistry, university of Edinburgh for mass spec analysis. We thank Juraj Bella in the NMR facility, School of Chemistry, University of Edinburgh for help with NMR experiments.

PY - 2024/11/11

Y1 - 2024/11/11

N2 - DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of DNMT3A1 with diverse modified nucleosomes indicative of different chromatin environments. A cryo-EM structure of the full-length DNMT3A1-DNMT3L complex with a H2AK119ub nucleosome reveals that the DNMT3A1 ubiquitin-dependent recruitment (UDR) motif interacts specifically with H2AK119ub and makes extensive contacts with the core nucleosome histone surface. This interaction facilitates robust DNMT3A1 binding to nucleosomes, and previously unexplained DNMT3A disease-associated mutations disrupt this interface. Furthermore, the UDR-nucleosome interaction synergises with other DNMT3A chromatin reading elements in the absence of histone ubiquitylation. H2AK119ub does not stimulate DNMT3A DNA methylation activity, as observed for the previously described H3K36me2 mark, which may explain low levels of DNA methylation on H2AK119ub marked facultative heterochromatin. This study highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome surface and increases our understanding of how DNMT3A1 chromatin recruitment occurs.

AB - DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of DNMT3A1 with diverse modified nucleosomes indicative of different chromatin environments. A cryo-EM structure of the full-length DNMT3A1-DNMT3L complex with a H2AK119ub nucleosome reveals that the DNMT3A1 ubiquitin-dependent recruitment (UDR) motif interacts specifically with H2AK119ub and makes extensive contacts with the core nucleosome histone surface. This interaction facilitates robust DNMT3A1 binding to nucleosomes, and previously unexplained DNMT3A disease-associated mutations disrupt this interface. Furthermore, the UDR-nucleosome interaction synergises with other DNMT3A chromatin reading elements in the absence of histone ubiquitylation. H2AK119ub does not stimulate DNMT3A DNA methylation activity, as observed for the previously described H3K36me2 mark, which may explain low levels of DNA methylation on H2AK119ub marked facultative heterochromatin. This study highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome surface and increases our understanding of how DNMT3A1 chromatin recruitment occurs.

KW - Chromatin

KW - Cryo-EM

KW - DNA methyltransferase

KW - Histone

KW - Epigenetic

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DO - 10.1038/s44319-024-00306-3

M3 - Article

SN - 1469-221X

JO - EMBO Reports

JF - EMBO Reports

ER -

The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.

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Keywords / Materials (for Non-textual outputs)

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The Hidden Cell Discovery Research Platform

Integrative Cell Mechanisms

Mechanistic understanding of the reading and writing of DNA methylation�

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The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

Access to Document

Other files and links

Fingerprint

Projects

The Hidden Cell Discovery Research Platform

Integrative Cell Mechanisms

Mechanistic understanding of the reading and writing of DNA methylation�

Cite this