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 Finan; Cristina Rubio-Ramon; Philippe Gautier; Hannah Wapenaar; Dhananjay Kumar; Hazel Davidson-Smith; Jimi Wills; Laura C. Murphy; Ann 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 Finan, Cristina Rubio-Ramon, Philippe Gautier, Hannah Wapenaar, Dhananjay Kumar, Hazel Davidson-Smith, Jimi Wills, Laura C. Murphy, Ann Wheeler, Marcus D. Wilson^*, Duncan Sproul^*

^*Corresponding author for this work

Psychological Sciences And Health

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

2 Citations (Scopus)

16 Downloads (Pure)

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 HP1α 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
Pages (from-to)	1130-1155
Number of pages	26
Journal	EMBO Reports
Volume	25
Issue number	3
Early online date	30 Jan 2024
DOIs	https://doi.org/10.1038/s44319-024-00061-5
Publication status	Published - 12 Mar 2024

Funding

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.

Keywords

DNA methylation
epigenetics
heterochromatin

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/s44319-024-00061-5Licence: CC BY 4.0

Taglini-etal-EMBOR-2024-DNMT3B-PWWP-mutations-cause-hypermethylationFinal published version, 4.39 MBLicence: CC BY 4.0

Cite this

Taglini, F., Kafetzopoulos, I., Rolls, W., Musialik, K. I., Lee, H. Y., Zhang, Y., Marenda, M., Kerr, L., Finan, H., Rubio-Ramon, C., Gautier, P., Wapenaar, H., Kumar, D., Davidson-Smith, H., Wills, J., Murphy, L. C., Wheeler, A., Wilson, M. D., & Sproul, D. (2024). DNMT3B PWWP mutations cause hypermethylation of heterochromatin. EMBO Reports, 25(3), 1130-1155. https://doi.org/10.1038/s44319-024-00061-5

@article{f9d383a4557c48998580ebff0dbe6d2c,

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 HP1α 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{\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.",

keywords = "DNA methylation, epigenetics, heterochromatin",

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

year = "2024",

month = mar,

day = "12",

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

language = "English",

volume = "25",

pages = "1130--1155",

number = "3",

}

Taglini, F, Kafetzopoulos, I, Rolls, W, Musialik, KI, Lee, HY, Zhang, Y, Marenda, M, Kerr, L, Finan, H, Rubio-Ramon, C, Gautier, P, Wapenaar, H, Kumar, D, Davidson-Smith, H, Wills, J, Murphy, LC, Wheeler, A, Wilson, MD & Sproul, D 2024, 'DNMT3B PWWP mutations cause hypermethylation of heterochromatin', EMBO Reports, vol. 25, no. 3, pp. 1130-1155. https://doi.org/10.1038/s44319-024-00061-5

TY - JOUR

T1 - DNMT3B PWWP mutations cause hypermethylation of heterochromatin

AU - Taglini, Francesca

AU - Kafetzopoulos, Ioannis

AU - Rolls, Willow

AU - Musialik, Kamila Irena

AU - Lee, Heng Yang

AU - Zhang, Yujie

AU - Marenda, Mattia

AU - Kerr, Lyndsay

AU - 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 C.

AU - Wheeler, Ann

AU - Wilson, Marcus D.

AU - Sproul, Duncan

PY - 2024/3/12

Y1 - 2024/3/12

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 HP1α 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.

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 HP1α 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.

KW - DNA methylation

KW - epigenetics

KW - heterochromatin

U2 - 10.1038/s44319-024-00061-5

DO - 10.1038/s44319-024-00061-5

M3 - Article

C2 - 38291337

AN - SCOPUS:85185294684

SN - 1469-221X

VL - 25

SP - 1130

EP - 1155

JO - EMBO Reports

JF - EMBO Reports

IS - 3

ER -

DNMT3B PWWP mutations cause hypermethylation of heterochromatin

Abstract

Funding

Keywords

UN SDGs

Access to Document

Fingerprint

Cite this