DNMT3B PWWP mutations cause hypermethylation of heterochromatin

Francesca Taglini; Ioannis Kafetzopoulos; Willow Rolls; Kamila Irena  Musialik; Heng  Yang Lee; Yujie  Zhang; Mattia Marenda; Lyndsay Kerr; Hannah M. Finan; Cristina Rubio Ramon; Philippe Gautier; Hannah Wapenaar; Dhananjay Kumar; Hazel Davidson-Smith; Jimi Wills; Laura Murphy; Ann P Wheeler; Marcus D Wilson; Duncan Sproul

doi:10.1038/s44319-024-00061-5

DNMT3B PWWP mutations cause hypermethylation of heterochromatin

Francesca Taglini, Ioannis Kafetzopoulos, Willow Rolls, Kamila Irena Musialik, Heng Yang Lee, Yujie Zhang, Mattia Marenda, Lyndsay Kerr, Hannah M. Finan, Cristina Rubio Ramon, Philippe Gautier, Hannah Wapenaar, Dhananjay Kumar, Hazel Davidson-Smith, Jimi Wills, Laura Murphy, Ann P Wheeler, Marcus D Wilson^*, Duncan Sproul^*

^*Corresponding author for this work

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

Abstract / Description of output

The correct establishment of DNA methylation patterns is vital for mammalian development and is
achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to
H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at
heterochromatin through an unknown recruitment mechanism. Here we find that knockout of
DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that
DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in
H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability
to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1 and
facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest
that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent manner
that is facilitated by the protein’s N-terminal region through an interaction with a key
heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation
homeostasis at heterochromatin, a process which is disrupted in cancer, aging and
Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.

Original language	English
Journal	EMBO Reports
DOIs	https://doi.org/10.1038/s44319-024-00061-5
Publication status	Published - 30 Jan 2024

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Taglini, F., Kafetzopoulos, I., Rolls, W., Musialik, K. I., Yang Lee, H., Zhang, Y., Marenda, M., Kerr, L., M. Finan, H., Rubio Ramon, C., Gautier, P., Wapenaar, H., Kumar, D., Davidson-Smith, H., Wills, J., Murphy, L., Wheeler, A. P., Wilson, M. D., & Sproul, D. (2024). DNMT3B PWWP mutations cause hypermethylation of heterochromatin. EMBO Reports. https://doi.org/10.1038/s44319-024-00061-5

@article{2f1d2efc65984157a34703b56bc90c4e,

title = "DNMT3B PWWP mutations cause hypermethylation of heterochromatin",

abstract = "The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1 and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent mannerthat is facilitated by the protein{\textquoteright}s N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.",

author = "Francesca Taglini and Ioannis Kafetzopoulos and Willow Rolls and Musialik, {Kamila Irena} and {Yang Lee}, Heng and Yujie Zhang and Mattia Marenda and Lyndsay Kerr and {M. Finan}, Hannah and {Rubio Ramon}, Cristina and Philippe Gautier and Hannah Wapenaar and Dhananjay Kumar and Hazel Davidson-Smith and Jimi Wills and Laura Murphy and Wheeler, {Ann P} and Wilson, {Marcus D} and Duncan Sproul",

note = "Funding Information: We thank C Uggenti, P Heyn, S Pelliciari, AP Jackson, Y Crow, S Janssen, M Lorincz and members of the Sproul and Wilson labs for useful discussions. We thank Edinburgh Clinical Research Facility Genetics Core, MRC IGC FACs and imaging core facilities for technical support. This work has made use of the resources provided by the University of Edinburgh digital research services and the MRC IGC compute cluster. Human histones were supplied from Addgene from the Landry lab. We thank Jeyaprakash Arulanandam, University of Edinburgh, for gift of the HP1 plasmid. We are grateful to Dhira Joshi at peptide chemistry at The Francis Crick Institute for the synthesis of H3 peptides. We thank Logan Mackay in SIRCAMS school of chemistry, University of Edinburgh for mass spec analysis. DS is a Cancer Research UK Career Development fellow (reference C47648/A20837), and work in his laboratory is also supported by an Medical Research Council university grant to the MRC Human Genetics Unit. MDW{\textquoteright}s work is supported by the Wellcome Trust (210493), Medical Research Council (T029471/1), and the University of Edinburgh. 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. IK was funded by a studentship from Cancer Research UK (C157/A25186) as well as the AG Leventis Foundation (18736). WR is funded by a PhD studentship from the Wellcome Trust (228154/Z/23/Z). LK is a cross-disciplinary post-doctoral fellow supported by funding from the University of Edinburgh and Medical Research Council (MC_UU_00009/2). HF was funded by an ERASMUS+ scholarship. DK is funded by the Darwin Trust of Edinburgh. Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = jan,

day = "30",

doi = "10.1038/s44319-024-00061-5",

language = "English",

journal = "EMBO Reports",

issn = "1469-221X",

publisher = "Wiley",

}

TY - JOUR

T1 - DNMT3B PWWP mutations cause hypermethylation of heterochromatin

AU - Taglini, Francesca

AU - Kafetzopoulos, Ioannis

AU - Rolls, Willow

AU - Musialik, Kamila Irena

AU - Yang Lee, Heng

AU - Zhang, Yujie

AU - Marenda, Mattia

AU - Kerr, Lyndsay

AU - M. Finan, Hannah

AU - Rubio Ramon, Cristina

AU - Gautier, Philippe

AU - Wapenaar, Hannah

AU - Kumar, Dhananjay

AU - Davidson-Smith, Hazel

AU - Wills, Jimi

AU - Murphy, Laura

AU - Wheeler, Ann P

AU - Wilson, Marcus D

AU - Sproul, Duncan

N1 - Funding Information: We thank C Uggenti, P Heyn, S Pelliciari, AP Jackson, Y Crow, S Janssen, M Lorincz and members of the Sproul and Wilson labs for useful discussions. We thank Edinburgh Clinical Research Facility Genetics Core, MRC IGC FACs and imaging core facilities for technical support. This work has made use of the resources provided by the University of Edinburgh digital research services and the MRC IGC compute cluster. Human histones were supplied from Addgene from the Landry lab. We thank Jeyaprakash Arulanandam, University of Edinburgh, for gift of the HP1 plasmid. We are grateful to Dhira Joshi at peptide chemistry at The Francis Crick Institute for the synthesis of H3 peptides. We thank Logan Mackay in SIRCAMS school of chemistry, University of Edinburgh for mass spec analysis. DS is a Cancer Research UK Career Development fellow (reference C47648/A20837), and work in his laboratory is also supported by an Medical Research Council university grant to the MRC Human Genetics Unit. MDW’s work is supported by the Wellcome Trust (210493), Medical Research Council (T029471/1), and the University of Edinburgh. 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. IK was funded by a studentship from Cancer Research UK (C157/A25186) as well as the AG Leventis Foundation (18736). WR is funded by a PhD studentship from the Wellcome Trust (228154/Z/23/Z). LK is a cross-disciplinary post-doctoral fellow supported by funding from the University of Edinburgh and Medical Research Council (MC_UU_00009/2). HF was funded by an ERASMUS+ scholarship. DK is funded by the Darwin Trust of Edinburgh. Publisher Copyright: © The Author(s) 2024.

PY - 2024/1/30

Y1 - 2024/1/30

N2 - The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1 and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent mannerthat is facilitated by the protein’s N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.

AB - The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1 and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent mannerthat is facilitated by the protein’s N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.

U2 - 10.1038/s44319-024-00061-5

DO - 10.1038/s44319-024-00061-5

M3 - Article

SN - 1469-221X

JO - EMBO Reports

JF - EMBO Reports

ER -

DNMT3B PWWP mutations cause hypermethylation of heterochromatin

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