Topoisomerase 1-dependent R-loop deficiency drives accelerated replication and genomic instability

Dan Sarni; Sonia Barroso; Alon Shtrikman; Michal Irony-Tur Sinai; Yifat S. Oren; Andrés Aguilera; Batsheva Kerem

doi:10.1016/j.celrep.2022.111397

Topoisomerase 1-dependent R-loop deficiency drives accelerated replication and genomic instability

Dan Sarni, Sonia Barroso, Alon Shtrikman, Michal Irony-Tur Sinai, Yifat S. Oren, Andrés Aguilera, Batsheva Kerem^*

^*Corresponding author for this work

Department of Genetics

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

1 Scopus citations

Abstract

DNA replication is a complex process tightly regulated to ensure faithful genome duplication, and its perturbation leads to DNA damage and genomic instability. Replication stress is commonly associated with slow and stalled replication forks. Recently, accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here, we show that mutated HRAS activation leads to increased topoisomerase 1 (TOP1) expression, causing aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids or R-loops. In these cells, restoration of TOP1 expression or mild replication inhibition rescues the perturbed replication and reduces DNA damage. Furthermore, TOP1 or RNaseH1 overexpression induces accelerated replication and DNA damage, highlighting the importance of TOP1 equilibrium in regulating R-loop homeostasis to ensure faithful DNA replication and genome integrity. Altogether, our results dissect a mechanism of oncogene-induced DNA damage by aberrant replication fork acceleration.

Original language	American English
Article number	111397
Journal	Cell Reports
Volume	40
Issue number	13
DOIs	https://doi.org/10.1016/j.celrep.2022.111397
State	Published - 27 Sep 2022

Bibliographical note

Funding Information:
This research was supported by grants from the Israel Science Foundation (grant nos. 176/11 and 1284/18 ), the Israeli Centers of Research Excellence ( I-CORE ), and Gene Regulation in Complex Human Disease, Center No. 41/11, and by the ISF- NSFC joint program (grant no. 2535/16 ) to B.K. and by grants from the Agencia Estatal de Investigación from the Spanish Ministry of Science and Innovation ( PID2019-104270GB-I00/BMC ), the European Research Council ( ERC2014 AdG669898 TARLOOP), the European Union ( FEDER ), and the Foundation “ Vencer el Cancer ” to A.A. The authors thank Dr. Naomi Melamed-Book for her assistance in confocal microscopy and the Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, for assistance in deep sequencing and bioinformatics analysis. The authors thank the members of the Kerem lab for thoughtful discussions and advice.

Funding Information:
This research was supported by grants from the Israel Science Foundation (grant nos. 176/11 and 1284/18), the Israeli Centers of Research Excellence (I-CORE), and Gene Regulation in Complex Human Disease, Center No. 41/11, and by the ISF-NSFC joint program (grant no. 2535/16) to B.K. and by grants from the Agencia Estatal de Investigación from the Spanish Ministry of Science and Innovation (PID2019-104270GB-I00/BMC), the European Research Council (ERC2014 AdG669898 TARLOOP), the European Union (FEDER), and the Foundation “Vencer el Cancer” to A.A. The authors thank Dr. Naomi Melamed-Book for her assistance in confocal microscopy and the Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, for assistance in deep sequencing and bioinformatics analysis. The authors thank the members of the Kerem lab for thoughtful discussions and advice. Conceptualization, D.S. and B.K.; methodology, D.S. A.A. and B.K.; investigation, D.S. S.B. A.S. M.I.-T.S. Y.S.O. A.A. and B.K.; visualization, D.S. and B.K.; writing – original draft, D.S. and B.K.; writing – review & editing, D.S. M.I.-T.S. A.A. and B.K.; funding acquisition, A.A. and B.K. The authors declare no competing interests.

Publisher Copyright:
© 2022 The Author(s)

Keywords

CP: Molecular biology
DNA replication
R loops
genomic instability
oncogenes
replication stress
topoisomerase 1

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10.1016/j.celrep.2022.111397

Cite this

@article{b0a4c81ed2214136918de0d9858aeb7a,

title = "Topoisomerase 1-dependent R-loop deficiency drives accelerated replication and genomic instability",

abstract = "DNA replication is a complex process tightly regulated to ensure faithful genome duplication, and its perturbation leads to DNA damage and genomic instability. Replication stress is commonly associated with slow and stalled replication forks. Recently, accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here, we show that mutated HRAS activation leads to increased topoisomerase 1 (TOP1) expression, causing aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids or R-loops. In these cells, restoration of TOP1 expression or mild replication inhibition rescues the perturbed replication and reduces DNA damage. Furthermore, TOP1 or RNaseH1 overexpression induces accelerated replication and DNA damage, highlighting the importance of TOP1 equilibrium in regulating R-loop homeostasis to ensure faithful DNA replication and genome integrity. Altogether, our results dissect a mechanism of oncogene-induced DNA damage by aberrant replication fork acceleration.",

keywords = "CP: Molecular biology, DNA replication, R loops, genomic instability, oncogenes, replication stress, topoisomerase 1",

author = "Dan Sarni and Sonia Barroso and Alon Shtrikman and {Irony-Tur Sinai}, Michal and Oren, {Yifat S.} and Andr{\'e}s Aguilera and Batsheva Kerem",

note = "Funding Information: This research was supported by grants from the Israel Science Foundation (grant nos. 176/11 and 1284/18 ), the Israeli Centers of Research Excellence ( I-CORE ), and Gene Regulation in Complex Human Disease, Center No. 41/11, and by the ISF- NSFC joint program (grant no. 2535/16 ) to B.K. and by grants from the Agencia Estatal de Investigaci{\'o}n from the Spanish Ministry of Science and Innovation ( PID2019-104270GB-I00/BMC ), the European Research Council ( ERC2014 AdG669898 TARLOOP), the European Union ( FEDER ), and the Foundation “ Vencer el Cancer ” to A.A. The authors thank Dr. Naomi Melamed-Book for her assistance in confocal microscopy and the Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, for assistance in deep sequencing and bioinformatics analysis. The authors thank the members of the Kerem lab for thoughtful discussions and advice. Funding Information: This research was supported by grants from the Israel Science Foundation (grant nos. 176/11 and 1284/18), the Israeli Centers of Research Excellence (I-CORE), and Gene Regulation in Complex Human Disease, Center No. 41/11, and by the ISF-NSFC joint program (grant no. 2535/16) to B.K. and by grants from the Agencia Estatal de Investigaci{\'o}n from the Spanish Ministry of Science and Innovation (PID2019-104270GB-I00/BMC), the European Research Council (ERC2014 AdG669898 TARLOOP), the European Union (FEDER), and the Foundation “Vencer el Cancer” to A.A. The authors thank Dr. Naomi Melamed-Book for her assistance in confocal microscopy and the Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, for assistance in deep sequencing and bioinformatics analysis. The authors thank the members of the Kerem lab for thoughtful discussions and advice. Conceptualization, D.S. and B.K.; methodology, D.S. A.A. and B.K.; investigation, D.S. S.B. A.S. M.I.-T.S. Y.S.O. A.A. and B.K.; visualization, D.S. and B.K.; writing – original draft, D.S. and B.K.; writing – review & editing, D.S. M.I.-T.S. A.A. and B.K.; funding acquisition, A.A. and B.K. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2022 The Author(s)",

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AU - Barroso, Sonia

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AU - Irony-Tur Sinai, Michal

AU - Oren, Yifat S.

AU - Aguilera, Andrés

AU - Kerem, Batsheva

N1 - Funding Information: This research was supported by grants from the Israel Science Foundation (grant nos. 176/11 and 1284/18 ), the Israeli Centers of Research Excellence ( I-CORE ), and Gene Regulation in Complex Human Disease, Center No. 41/11, and by the ISF- NSFC joint program (grant no. 2535/16 ) to B.K. and by grants from the Agencia Estatal de Investigación from the Spanish Ministry of Science and Innovation ( PID2019-104270GB-I00/BMC ), the European Research Council ( ERC2014 AdG669898 TARLOOP), the European Union ( FEDER ), and the Foundation “ Vencer el Cancer ” to A.A. The authors thank Dr. Naomi Melamed-Book for her assistance in confocal microscopy and the Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, for assistance in deep sequencing and bioinformatics analysis. The authors thank the members of the Kerem lab for thoughtful discussions and advice. Funding Information: This research was supported by grants from the Israel Science Foundation (grant nos. 176/11 and 1284/18), the Israeli Centers of Research Excellence (I-CORE), and Gene Regulation in Complex Human Disease, Center No. 41/11, and by the ISF-NSFC joint program (grant no. 2535/16) to B.K. and by grants from the Agencia Estatal de Investigación from the Spanish Ministry of Science and Innovation (PID2019-104270GB-I00/BMC), the European Research Council (ERC2014 AdG669898 TARLOOP), the European Union (FEDER), and the Foundation “Vencer el Cancer” to A.A. The authors thank Dr. Naomi Melamed-Book for her assistance in confocal microscopy and the Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, for assistance in deep sequencing and bioinformatics analysis. The authors thank the members of the Kerem lab for thoughtful discussions and advice. Conceptualization, D.S. and B.K.; methodology, D.S. A.A. and B.K.; investigation, D.S. S.B. A.S. M.I.-T.S. Y.S.O. A.A. and B.K.; visualization, D.S. and B.K.; writing – original draft, D.S. and B.K.; writing – review & editing, D.S. M.I.-T.S. A.A. and B.K.; funding acquisition, A.A. and B.K. The authors declare no competing interests. Publisher Copyright: © 2022 The Author(s)

PY - 2022/9/27

Y1 - 2022/9/27

N2 - DNA replication is a complex process tightly regulated to ensure faithful genome duplication, and its perturbation leads to DNA damage and genomic instability. Replication stress is commonly associated with slow and stalled replication forks. Recently, accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here, we show that mutated HRAS activation leads to increased topoisomerase 1 (TOP1) expression, causing aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids or R-loops. In these cells, restoration of TOP1 expression or mild replication inhibition rescues the perturbed replication and reduces DNA damage. Furthermore, TOP1 or RNaseH1 overexpression induces accelerated replication and DNA damage, highlighting the importance of TOP1 equilibrium in regulating R-loop homeostasis to ensure faithful DNA replication and genome integrity. Altogether, our results dissect a mechanism of oncogene-induced DNA damage by aberrant replication fork acceleration.

AB - DNA replication is a complex process tightly regulated to ensure faithful genome duplication, and its perturbation leads to DNA damage and genomic instability. Replication stress is commonly associated with slow and stalled replication forks. Recently, accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here, we show that mutated HRAS activation leads to increased topoisomerase 1 (TOP1) expression, causing aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids or R-loops. In these cells, restoration of TOP1 expression or mild replication inhibition rescues the perturbed replication and reduces DNA damage. Furthermore, TOP1 or RNaseH1 overexpression induces accelerated replication and DNA damage, highlighting the importance of TOP1 equilibrium in regulating R-loop homeostasis to ensure faithful DNA replication and genome integrity. Altogether, our results dissect a mechanism of oncogene-induced DNA damage by aberrant replication fork acceleration.

KW - CP: Molecular biology

KW - DNA replication

KW - R loops

KW - genomic instability

KW - oncogenes

KW - replication stress

KW - topoisomerase 1

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U2 - 10.1016/j.celrep.2022.111397

DO - 10.1016/j.celrep.2022.111397

M3 - Article

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AN - SCOPUS:85138795853

SN - 2211-1247

VL - 40

JO - Cell Reports

JF - Cell Reports

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ER -

Topoisomerase 1-dependent R-loop deficiency drives accelerated replication and genomic instability

Abstract

Bibliographical note

Keywords

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