H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ

Rachel Bayley; Valerie Borel; Rhiannon Moss; Ellie Sweatman; Philip Ruis; Alice Ormrod; Amalia Goula; Rachel Mottram; Tyler Stanage; Graeme Hewitt; Marco Saponaro; Grant Stewart; Simon Boulton; Martin Higgs

doi:10.1016/j.molcel.2022.03.030

H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ

Rachel Bayley, Valerie Borel, Rhiannon Moss, Ellie Sweatman, Philip Ruis, Alice Ormrod, Amalia Goula, Rachel Mottram, Tyler Stanage, Graeme Hewitt, Marco Saponaro, Grant Stewart, Simon Boulton, Martin Higgs^*

^*Corresponding author for this work

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

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Abstract

The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.

Original language	English
Pages (from-to)	1924-1939.e10
Number of pages	26
Journal	Molecular Cell
Volume	82
Issue number	10
Early online date	18 Apr 2022
DOIs	https://doi.org/10.1016/j.molcel.2022.03.030
Publication status	Published - 19 May 2022

Bibliographical note

Funding Information:
We thank Clare Davies, Jo Morris, and other members of the Birmingham Centre for Genome Biology (BCGB) for invaluable discussions. We are grateful to Robert Klose for providing KDM5A expression reagents and Graham Dellaire for providing plasmids for the CRISPR-based HR assay. We thank the Crick BRF and GEMs for support with animal production and experiments. R.B. was funded by a Birmingham Fellowship and a Wellcome Institutional Strategic Support Fund (204846/Z/16/Z) awarded to M.R.H. by the University of Birmingham. E.S. is funded by the University of Birmingham and supported by Cancer Research UK (C17422/A25154). R.M.A.M. was funded by the UK Medical Research Council and University of Birmingham. M.R.H. A.O. and A.G. are funded by a UK Medical Research Council Career Development Fellowship (MR/P009085/1). M.S. is supported by a Birmingham Fellowship, the Wellcome Trust (202115/Z/16/Z), Royal Society (RG170246), and BBSRC (BB/S016155/1). G.S.S. is funded by a CR-UK Programme Grant (C17183/A23303). S.J.B. P.R. T.S. and V.B. are supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC0010048), the UK Medical Research Council (FC0010048), and the Wellcome Trust (FC0010048). S.J.B. is also funded by a European Research Council (ERC) Advanced Investigator Grant (TelMetab) and Wellcome Trust Senior Investigator and Collaborative Grants. Conceptualization, M.R.H. G.S.S. and S.J.B.; investigation, R.B. V.B. R.J.M. E.S. P.R. A.O. A.G. R.M.A.M. M.S. G.S.S. and M.R.H.; resources, T.S. and G.H.; writing—original draft, R.B. V.B. S.J.B. and M.R.H. with comments from all authors; writing—review & editing, M.R.H. S.J.B. and R.B.; funding acquisition, M.R.H. G.S.S. and S.J.B.; supervision, M.R.H. G.S.S. and S.J.B. S.J.B. is a co-founder and VP in Science Strategy at Artios Pharma and is a member of the Molecular Cell advisory board. The authors declare no other competing interests.

Publisher Copyright:
© 2022 The Author(s)

Keywords

double-strand break repair
53BP1
RIF1
shieldin
SETD1A
H3K4 methylation
BOD1L
class switch recombination
PARP inhibitors

ASJC Scopus subject areas

Molecular Biology
Cell Biology

Access to Document

10.1016/j.molcel.2022.03.030Licence: Creative Commons: Attribution (CC BY)

BayleyR2022H3K4Final published version, 4.69 MBLicence: Creative Commons: Attribution (CC BY)

1 Active
3 Finished

Characterising novel regulators of the PI-3-kinase-like kinase-dependent DNA damage response and their role in preventing human disease and cancer
Stewart, G. (Principal Investigator)
Cancer Research Uk
1/09/17 → 31/05/25
Project: Research
Characterisation of the global coordination of DNA replication and transcription
Saponaro, M. (Principal Investigator)
The Royal Society
1/11/17 → 31/10/18
Project: Research Councils
The impact of non-histone protein methylation by set1a in maintaining genome stability and preventing disease
Higgs, M. (Principal Investigator)
Medical Research Council
1/04/17 → 31/03/23
Project: Research Councils
RNA Pol II subunits in the regulation of transcription and genome instability
Saponaro, M. (Principal Investigator)
The Wellcome Trust
1/10/16 → 30/09/18
Project: Research

Cite this

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title = "H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ",

abstract = "The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.",

keywords = "double-strand break repair, 53BP1, RIF1, shieldin, SETD1A, H3K4 methylation, BOD1L, class switch recombination, PARP inhibitors",

author = "Rachel Bayley and Valerie Borel and Rhiannon Moss and Ellie Sweatman and Philip Ruis and Alice Ormrod and Amalia Goula and Rachel Mottram and Tyler Stanage and Graeme Hewitt and Marco Saponaro and Grant Stewart and Simon Boulton and Martin Higgs",

note = "Funding Information: We thank Clare Davies, Jo Morris, and other members of the Birmingham Centre for Genome Biology (BCGB) for invaluable discussions. We are grateful to Robert Klose for providing KDM5A expression reagents and Graham Dellaire for providing plasmids for the CRISPR-based HR assay. We thank the Crick BRF and GEMs for support with animal production and experiments. R.B. was funded by a Birmingham Fellowship and a Wellcome Institutional Strategic Support Fund (204846/Z/16/Z) awarded to M.R.H. by the University of Birmingham. E.S. is funded by the University of Birmingham and supported by Cancer Research UK (C17422/A25154). R.M.A.M. was funded by the UK Medical Research Council and University of Birmingham. M.R.H. A.O. and A.G. are funded by a UK Medical Research Council Career Development Fellowship (MR/P009085/1). M.S. is supported by a Birmingham Fellowship, the Wellcome Trust (202115/Z/16/Z), Royal Society (RG170246), and BBSRC (BB/S016155/1). G.S.S. is funded by a CR-UK Programme Grant (C17183/A23303). S.J.B. P.R. T.S. and V.B. are supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC0010048), the UK Medical Research Council (FC0010048), and the Wellcome Trust (FC0010048). S.J.B. is also funded by a European Research Council (ERC) Advanced Investigator Grant (TelMetab) and Wellcome Trust Senior Investigator and Collaborative Grants. Conceptualization, M.R.H. G.S.S. and S.J.B.; investigation, R.B. V.B. R.J.M. E.S. P.R. A.O. A.G. R.M.A.M. M.S. G.S.S. and M.R.H.; resources, T.S. and G.H.; writing—original draft, R.B. V.B. S.J.B. and M.R.H. with comments from all authors; writing—review & editing, M.R.H. S.J.B. and R.B.; funding acquisition, M.R.H. G.S.S. and S.J.B.; supervision, M.R.H. G.S.S. and S.J.B. S.J.B. is a co-founder and VP in Science Strategy at Artios Pharma and is a member of the Molecular Cell advisory board. The authors declare no other competing interests. Publisher Copyright: {\textcopyright} 2022 The Author(s)",

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T1 - H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ

AU - Bayley, Rachel

AU - Borel, Valerie

AU - Moss, Rhiannon

AU - Sweatman, Ellie

AU - Ruis, Philip

AU - Ormrod, Alice

AU - Goula, Amalia

AU - Mottram, Rachel

AU - Stanage, Tyler

AU - Hewitt, Graeme

AU - Saponaro, Marco

AU - Stewart, Grant

AU - Boulton, Simon

AU - Higgs, Martin

N1 - Funding Information: We thank Clare Davies, Jo Morris, and other members of the Birmingham Centre for Genome Biology (BCGB) for invaluable discussions. We are grateful to Robert Klose for providing KDM5A expression reagents and Graham Dellaire for providing plasmids for the CRISPR-based HR assay. We thank the Crick BRF and GEMs for support with animal production and experiments. R.B. was funded by a Birmingham Fellowship and a Wellcome Institutional Strategic Support Fund (204846/Z/16/Z) awarded to M.R.H. by the University of Birmingham. E.S. is funded by the University of Birmingham and supported by Cancer Research UK (C17422/A25154). R.M.A.M. was funded by the UK Medical Research Council and University of Birmingham. M.R.H. A.O. and A.G. are funded by a UK Medical Research Council Career Development Fellowship (MR/P009085/1). M.S. is supported by a Birmingham Fellowship, the Wellcome Trust (202115/Z/16/Z), Royal Society (RG170246), and BBSRC (BB/S016155/1). G.S.S. is funded by a CR-UK Programme Grant (C17183/A23303). S.J.B. P.R. T.S. and V.B. are supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC0010048), the UK Medical Research Council (FC0010048), and the Wellcome Trust (FC0010048). S.J.B. is also funded by a European Research Council (ERC) Advanced Investigator Grant (TelMetab) and Wellcome Trust Senior Investigator and Collaborative Grants. Conceptualization, M.R.H. G.S.S. and S.J.B.; investigation, R.B. V.B. R.J.M. E.S. P.R. A.O. A.G. R.M.A.M. M.S. G.S.S. and M.R.H.; resources, T.S. and G.H.; writing—original draft, R.B. V.B. S.J.B. and M.R.H. with comments from all authors; writing—review & editing, M.R.H. S.J.B. and R.B.; funding acquisition, M.R.H. G.S.S. and S.J.B.; supervision, M.R.H. G.S.S. and S.J.B. S.J.B. is a co-founder and VP in Science Strategy at Artios Pharma and is a member of the Molecular Cell advisory board. The authors declare no other competing interests. Publisher Copyright: © 2022 The Author(s)

PY - 2022/5/19

Y1 - 2022/5/19

N2 - The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.

AB - The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.

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KW - RIF1

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KW - SETD1A

KW - H3K4 methylation

KW - BOD1L

KW - class switch recombination

KW - PARP inhibitors

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DO - 10.1016/j.molcel.2022.03.030

M3 - Article

C2 - 35439434

AN - SCOPUS:85130189893

SN - 1097-2765

VL - 82

SP - 1924-1939.e10

JO - Molecular Cell

JF - Molecular Cell

IS - 10

ER -

H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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Projects

Characterising novel regulators of the PI-3-kinase-like kinase-dependent DNA damage response and their role in preventing human disease and cancer

Characterisation of the global coordination of DNA replication and transcription

The impact of non-histone protein methylation by set1a in maintaining genome stability and preventing disease

RNA Pol II subunits in the regulation of transcription and genome instability

Cite this