The fork protection complex promotes parental histone recycling and epigenetic memory

Sebastian Jespersen Charlton; Valentin Flury; Yutaka Kanoh; Aitana Victoria Genzor; Leonie Kollenstart; Wantong Ao; Peter Brøgger; Melanie Bianca Weisser; Marek Adamus; Nicolas Alcaraz; Charlotte M. Delvaux de Fenffe; Francesca Mattiroli; Guillermo Montoya; Hisao Masai; Anja Groth; Geneviève Thon

doi:10.1016/j.cell.2024.07.017

The fork protection complex promotes parental histone recycling and epigenetic memory

Sebastian Jespersen Charlton, Valentin Flury, Yutaka Kanoh, Aitana Victoria Genzor, Leonie Kollenstart, Wantong Ao, Peter Brøgger, Melanie Bianca Weisser, Marek Adamus, Nicolas Alcaraz, Charlotte M. Delvaux de Fenffe, Francesca Mattiroli, Guillermo Montoya, Hisao Masai, Anja Groth^*, Geneviève Thon^*

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

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Abstract

The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (CLASPIN in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. Both mutants showed clonal and asymmetric loss of H3K9me-mediated gene silencing. AlphaFold predicted co-chaperoning of H3-H4 tetramers by Mrc1 and Mcm2, with the Mrc1 connector domain bridging histone and Mcm2 binding. Biochemical and functional analysis validated this model and revealed a duality in Mrc1 function: disabling histone binding in the connector domain disrupted lagging-strand recycling while another histone-binding mutation impaired leading strand recycling. We propose that Mrc1 toggles histones between the lagging and leading strand recycling pathways, in part by intra-replisome co-chaperoning, to ensure epigenetic transmission to both daughter cells.

Original language	English
Journal	Cell
Volume	187
Issue number	18
Pages (from-to)	5029-5047
Number of pages	41
ISSN	0092-8674
DOIs	https://doi.org/10.1016/j.cell.2024.07.017
Publication status	Published - 2024

Bibliographical note

Funding Information:
We thank Paul Russell for strains, Naoki Horikoshi and Hitoshi Kurumizaka for human histone H3.1-H4 tetramer, Katsunori Tanaka for sharing unpublished data, Danesh Moazed for sharing information prior to publication, Jose Rafael Ciges Tomas for advice, members of our labs for discussions, and the CPR/reNEW Genomics platform and the CPR Protein Production and Characterization Platform for support. G.T. was supported by the Novo Nordisk Foundation (NNF19OC0058686) and Carlsberg Foundation (CF15-0853, CF19-0200, and CF22-1467). A.G. was supported by the Novo Nordisk Foundation (NNF21OC0067425) and Lundbeck Foundation (R313-2019-448). H.M. was supported by Grant-in-Aid for Scientific Research (A) (JSPS 20H00463) and by Research Support Project for Life Science and Drug Discovery from AMED (JP23ama121009). G.M. was supported by the Novo Nordisk Foundation (NNF0024386, NNF17SA0030214, and NNF18OC0055061) and ERC (ERC_AdG_101096548 INTETOOLS). G.M. is a member of the Integrative Structural Biology Cluster (ISBUC) at the University of Copenhagen. Research at CPR is supported by the Novo Nordisk Foundation (grant NNF14CC0001). S.J.C. was supported by the Danish Cancer Society (R318-A18520). F.M. is funded by an ERC StG (851564). S.J.C. V.F. A.V.G. L.K. H.M. A.G. and G.T. designed the experiments; S.J.C. V.F. A.V.G. L.K. W.A. Y.K. and P.B. conducted the experiments; M.B.W. M.A. and G.M. conducted AlphaFold predictions and contributed corresponding sections to the paper; N.A. performed bioinformatics analysis; C.M.D.d.F. and F.M. produced histones and advised on biochemistry; and S.J.C. V.F. A.G. and G.T. wrote the paper. A.G. is co-founder and chief scientific officer (CSO) of Ankrin Therapeutics. A.G. is a member of the scientific advisory board of Molecular Cell. G.M. is a stockholder of Ensoma and a member of its scientific advisory board. The other authors declare no competing interests.

Funding Information:
We thank Paul Russell for strains, Naoki Horikoshi and Hitoshi Kurumizaka for human histone H3.1-H4 tetramer, Katsunori Tanaka for sharing unpublished data, Danesh Moazed for sharing information prior to publication, Jose Rafael Ciges Tomas for advice, members of our labs for discussions, and the CPR/reNEW Genomics platform and the CPR Protein Production and Characterization Platform for support. G.T. was supported by the Novo Nordisk Foundation ( NNF19OC0058686 ) and Carlsberg Foundation ( CF15-0853 , CF19-0200 , and CF22-1467 ). A.G. was supported by the Novo Nordisk Foundation ( NNF21OC0067425 ) and Lundbeck Foundation ( R313-2019-448 ). H.M. was supported by Grant-in-Aid for Scientific Research (A) ( JSPS 20H00463 ) and by Research Support Project for Life Science and Drug Discovery from AMED ( JP23ama121009 ). G.M. was supported by the Novo Nordisk Foundation ( NNF0024386 , NNF17SA0030214 , and NNF18OC0055061 ) and ERC ( ERC_AdG_101096548 INTETOOLS ). G.M. is a member of the Integrative Structural Biology Cluster (ISBUC) at the University of Copenhagen . Research at CPR is supported by the Novo Nordisk Foundation (grant NNF14CC0001 ). S.J.C. was supported by the Danish Cancer Society ( R318-A18520 ). F.M. is funded by an ERC StG ( 851564 ).

Publisher Copyright:
© 2024 The Authors

Keywords

chromatin replication
Claspin
DNA replication
epigenetic inheritance
epigenome maintenance
fission yeast
H3K9 methylation
heterochromatin
histone chaperone
histone recycling
mouse embryonic stem cells

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Cite this

Charlton, S. J., Flury, V., Kanoh, Y., Genzor, A. V., Kollenstart, L., Ao, W., Brøgger, P., Weisser, M. B., Adamus, M., Alcaraz, N., Delvaux de Fenffe, C. M., Mattiroli, F., Montoya, G., Masai, H., Groth, A., & Thon, G. (2024). The fork protection complex promotes parental histone recycling and epigenetic memory. Cell, 187(18), 5029-5047. https://doi.org/10.1016/j.cell.2024.07.017

Charlton, SJ, Flury, V, Kanoh, Y, Genzor, AV, Kollenstart, L, Ao, W, Brøgger, P, Weisser, MB , Adamus, M, Alcaraz, N, Delvaux de Fenffe, CM, Mattiroli, F, Montoya, G, Masai, H, Groth, A & Thon, G 2024, 'The fork protection complex promotes parental histone recycling and epigenetic memory', Cell, vol. 187, no. 18, pp. 5029-5047. https://doi.org/10.1016/j.cell.2024.07.017

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title = "The fork protection complex promotes parental histone recycling and epigenetic memory",

abstract = "The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (CLASPIN in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. Both mutants showed clonal and asymmetric loss of H3K9me-mediated gene silencing. AlphaFold predicted co-chaperoning of H3-H4 tetramers by Mrc1 and Mcm2, with the Mrc1 connector domain bridging histone and Mcm2 binding. Biochemical and functional analysis validated this model and revealed a duality in Mrc1 function: disabling histone binding in the connector domain disrupted lagging-strand recycling while another histone-binding mutation impaired leading strand recycling. We propose that Mrc1 toggles histones between the lagging and leading strand recycling pathways, in part by intra-replisome co-chaperoning, to ensure epigenetic transmission to both daughter cells.",

keywords = "chromatin replication, Claspin, DNA replication, epigenetic inheritance, epigenome maintenance, fission yeast, H3K9 methylation, heterochromatin, histone chaperone, histone recycling, mouse embryonic stem cells",

author = "Charlton, {Sebastian Jespersen} and Valentin Flury and Yutaka Kanoh and Genzor, {Aitana Victoria} and Leonie Kollenstart and Wantong Ao and Peter Br{\o}gger and Weisser, {Melanie Bianca} and Marek Adamus and Nicolas Alcaraz and {Delvaux de Fenffe}, {Charlotte M.} and Francesca Mattiroli and Guillermo Montoya and Hisao Masai and Anja Groth and Genevi{\`e}ve Thon",

note = "Funding Information: We thank Paul Russell for strains, Naoki Horikoshi and Hitoshi Kurumizaka for human histone H3.1-H4 tetramer, Katsunori Tanaka for sharing unpublished data, Danesh Moazed for sharing information prior to publication, Jose Rafael Ciges Tomas for advice, members of our labs for discussions, and the CPR/reNEW Genomics platform and the CPR Protein Production and Characterization Platform for support. G.T. was supported by the Novo Nordisk Foundation (NNF19OC0058686) and Carlsberg Foundation (CF15-0853, CF19-0200, and CF22-1467). A.G. was supported by the Novo Nordisk Foundation (NNF21OC0067425) and Lundbeck Foundation (R313-2019-448). H.M. was supported by Grant-in-Aid for Scientific Research (A) (JSPS 20H00463) and by Research Support Project for Life Science and Drug Discovery from AMED (JP23ama121009). G.M. was supported by the Novo Nordisk Foundation (NNF0024386, NNF17SA0030214, and NNF18OC0055061) and ERC (ERC_AdG_101096548 INTETOOLS). G.M. is a member of the Integrative Structural Biology Cluster (ISBUC) at the University of Copenhagen. Research at CPR is supported by the Novo Nordisk Foundation (grant NNF14CC0001). S.J.C. was supported by the Danish Cancer Society (R318-A18520). F.M. is funded by an ERC StG (851564). S.J.C. V.F. A.V.G. L.K. H.M. A.G. and G.T. designed the experiments; S.J.C. V.F. A.V.G. L.K. W.A. Y.K. and P.B. conducted the experiments; M.B.W. M.A. and G.M. conducted AlphaFold predictions and contributed corresponding sections to the paper; N.A. performed bioinformatics analysis; C.M.D.d.F. and F.M. produced histones and advised on biochemistry; and S.J.C. V.F. A.G. and G.T. wrote the paper. A.G. is co-founder and chief scientific officer (CSO) of Ankrin Therapeutics. A.G. is a member of the scientific advisory board of Molecular Cell. G.M. is a stockholder of Ensoma and a member of its scientific advisory board. The other authors declare no competing interests. Funding Information: We thank Paul Russell for strains, Naoki Horikoshi and Hitoshi Kurumizaka for human histone H3.1-H4 tetramer, Katsunori Tanaka for sharing unpublished data, Danesh Moazed for sharing information prior to publication, Jose Rafael Ciges Tomas for advice, members of our labs for discussions, and the CPR/reNEW Genomics platform and the CPR Protein Production and Characterization Platform for support. G.T. was supported by the Novo Nordisk Foundation ( NNF19OC0058686 ) and Carlsberg Foundation ( CF15-0853 , CF19-0200 , and CF22-1467 ). A.G. was supported by the Novo Nordisk Foundation ( NNF21OC0067425 ) and Lundbeck Foundation ( R313-2019-448 ). H.M. was supported by Grant-in-Aid for Scientific Research (A) ( JSPS 20H00463 ) and by Research Support Project for Life Science and Drug Discovery from AMED ( JP23ama121009 ). G.M. was supported by the Novo Nordisk Foundation ( NNF0024386 , NNF17SA0030214 , and NNF18OC0055061 ) and ERC ( ERC_AdG_101096548 INTETOOLS ). G.M. is a member of the Integrative Structural Biology Cluster (ISBUC) at the University of Copenhagen . Research at CPR is supported by the Novo Nordisk Foundation (grant NNF14CC0001 ). S.J.C. was supported by the Danish Cancer Society ( R318-A18520 ). F.M. is funded by an ERC StG ( 851564 ). Publisher Copyright: {\textcopyright} 2024 The Authors",

year = "2024",

doi = "10.1016/j.cell.2024.07.017",

language = "English",

volume = "187",

pages = "5029--5047",

journal = "Cell",

issn = "0092-8674",

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TY - JOUR

T1 - The fork protection complex promotes parental histone recycling and epigenetic memory

AU - Charlton, Sebastian Jespersen

AU - Flury, Valentin

AU - Kanoh, Yutaka

AU - Genzor, Aitana Victoria

AU - Kollenstart, Leonie

AU - Ao, Wantong

AU - Brøgger, Peter

AU - Weisser, Melanie Bianca

AU - Adamus, Marek

AU - Alcaraz, Nicolas

AU - Delvaux de Fenffe, Charlotte M.

AU - Mattiroli, Francesca

AU - Montoya, Guillermo

AU - Masai, Hisao

AU - Groth, Anja

AU - Thon, Geneviève

N1 - Funding Information: We thank Paul Russell for strains, Naoki Horikoshi and Hitoshi Kurumizaka for human histone H3.1-H4 tetramer, Katsunori Tanaka for sharing unpublished data, Danesh Moazed for sharing information prior to publication, Jose Rafael Ciges Tomas for advice, members of our labs for discussions, and the CPR/reNEW Genomics platform and the CPR Protein Production and Characterization Platform for support. G.T. was supported by the Novo Nordisk Foundation (NNF19OC0058686) and Carlsberg Foundation (CF15-0853, CF19-0200, and CF22-1467). A.G. was supported by the Novo Nordisk Foundation (NNF21OC0067425) and Lundbeck Foundation (R313-2019-448). H.M. was supported by Grant-in-Aid for Scientific Research (A) (JSPS 20H00463) and by Research Support Project for Life Science and Drug Discovery from AMED (JP23ama121009). G.M. was supported by the Novo Nordisk Foundation (NNF0024386, NNF17SA0030214, and NNF18OC0055061) and ERC (ERC_AdG_101096548 INTETOOLS). G.M. is a member of the Integrative Structural Biology Cluster (ISBUC) at the University of Copenhagen. Research at CPR is supported by the Novo Nordisk Foundation (grant NNF14CC0001). S.J.C. was supported by the Danish Cancer Society (R318-A18520). F.M. is funded by an ERC StG (851564). S.J.C. V.F. A.V.G. L.K. H.M. A.G. and G.T. designed the experiments; S.J.C. V.F. A.V.G. L.K. W.A. Y.K. and P.B. conducted the experiments; M.B.W. M.A. and G.M. conducted AlphaFold predictions and contributed corresponding sections to the paper; N.A. performed bioinformatics analysis; C.M.D.d.F. and F.M. produced histones and advised on biochemistry; and S.J.C. V.F. A.G. and G.T. wrote the paper. A.G. is co-founder and chief scientific officer (CSO) of Ankrin Therapeutics. A.G. is a member of the scientific advisory board of Molecular Cell. G.M. is a stockholder of Ensoma and a member of its scientific advisory board. The other authors declare no competing interests. Funding Information: We thank Paul Russell for strains, Naoki Horikoshi and Hitoshi Kurumizaka for human histone H3.1-H4 tetramer, Katsunori Tanaka for sharing unpublished data, Danesh Moazed for sharing information prior to publication, Jose Rafael Ciges Tomas for advice, members of our labs for discussions, and the CPR/reNEW Genomics platform and the CPR Protein Production and Characterization Platform for support. G.T. was supported by the Novo Nordisk Foundation ( NNF19OC0058686 ) and Carlsberg Foundation ( CF15-0853 , CF19-0200 , and CF22-1467 ). A.G. was supported by the Novo Nordisk Foundation ( NNF21OC0067425 ) and Lundbeck Foundation ( R313-2019-448 ). H.M. was supported by Grant-in-Aid for Scientific Research (A) ( JSPS 20H00463 ) and by Research Support Project for Life Science and Drug Discovery from AMED ( JP23ama121009 ). G.M. was supported by the Novo Nordisk Foundation ( NNF0024386 , NNF17SA0030214 , and NNF18OC0055061 ) and ERC ( ERC_AdG_101096548 INTETOOLS ). G.M. is a member of the Integrative Structural Biology Cluster (ISBUC) at the University of Copenhagen . Research at CPR is supported by the Novo Nordisk Foundation (grant NNF14CC0001 ). S.J.C. was supported by the Danish Cancer Society ( R318-A18520 ). F.M. is funded by an ERC StG ( 851564 ). Publisher Copyright: © 2024 The Authors

PY - 2024

Y1 - 2024

N2 - The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (CLASPIN in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. Both mutants showed clonal and asymmetric loss of H3K9me-mediated gene silencing. AlphaFold predicted co-chaperoning of H3-H4 tetramers by Mrc1 and Mcm2, with the Mrc1 connector domain bridging histone and Mcm2 binding. Biochemical and functional analysis validated this model and revealed a duality in Mrc1 function: disabling histone binding in the connector domain disrupted lagging-strand recycling while another histone-binding mutation impaired leading strand recycling. We propose that Mrc1 toggles histones between the lagging and leading strand recycling pathways, in part by intra-replisome co-chaperoning, to ensure epigenetic transmission to both daughter cells.

AB - The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (CLASPIN in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. Both mutants showed clonal and asymmetric loss of H3K9me-mediated gene silencing. AlphaFold predicted co-chaperoning of H3-H4 tetramers by Mrc1 and Mcm2, with the Mrc1 connector domain bridging histone and Mcm2 binding. Biochemical and functional analysis validated this model and revealed a duality in Mrc1 function: disabling histone binding in the connector domain disrupted lagging-strand recycling while another histone-binding mutation impaired leading strand recycling. We propose that Mrc1 toggles histones between the lagging and leading strand recycling pathways, in part by intra-replisome co-chaperoning, to ensure epigenetic transmission to both daughter cells.

KW - chromatin replication

KW - Claspin

KW - DNA replication

KW - epigenetic inheritance

KW - epigenome maintenance

KW - fission yeast

KW - H3K9 methylation

KW - heterochromatin

KW - histone chaperone

KW - histone recycling

KW - mouse embryonic stem cells

U2 - 10.1016/j.cell.2024.07.017

DO - 10.1016/j.cell.2024.07.017

M3 - Journal article

C2 - 39094569

AN - SCOPUS:85201712321

SN - 0092-8674

VL - 187

SP - 5029

EP - 5047

JO - Cell

JF - Cell

IS - 18

ER -