Molecular dependencies and genomic consequences of a global DNA damage tolerance defect
Abstract Background DNA damage tolerance (DDT) enables replication to continue in the presence of fork stalling lesions. In mammalian cells, DDT is regulated by two independent pathways, controlled by the polymerase REV1 and ubiquitinated PCNA, respectively. Results To determine the molecular and ge...
Saved in:
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-12-01
|
| Series: | Genome Biology |
| Online Access: | https://doi.org/10.1186/s13059-024-03451-z |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559387899953152 |
|---|---|
| author | Daniel de Groot Aldo Spanjaard Ronak Shah Maaike Kreft Ben Morris Cor Lieftink Joyce J. I. Catsman Shirley Ormel Matilda Ayidah Bas Pilzecker Olimpia Alessandra Buoninfante Paul C. M. van den Berk Roderick L. Beijersbergen Heinz Jacobs |
| author_facet | Daniel de Groot Aldo Spanjaard Ronak Shah Maaike Kreft Ben Morris Cor Lieftink Joyce J. I. Catsman Shirley Ormel Matilda Ayidah Bas Pilzecker Olimpia Alessandra Buoninfante Paul C. M. van den Berk Roderick L. Beijersbergen Heinz Jacobs |
| author_sort | Daniel de Groot |
| collection | DOAJ |
| description | Abstract Background DNA damage tolerance (DDT) enables replication to continue in the presence of fork stalling lesions. In mammalian cells, DDT is regulated by two independent pathways, controlled by the polymerase REV1 and ubiquitinated PCNA, respectively. Results To determine the molecular and genomic impact of a global DDT defect, we studied PcnaK164R/−;Rev1−/− compound mutants in mouse cells. Double-mutant cells display increased replication stress, hypersensitivity to genotoxic agents, replication speed, and repriming. A whole-genome CRISPR-Cas9 screen revealed a strict reliance of double-mutant cells on the CST complex, where CST promotes fork stability. Whole-genome sequencing indicated that this double-mutant DDT defect favors the generation of large, replication-stress inducible deletions of 0.4–4.0 kbp, defined as type 3 deletions. Junction break sites of these deletions reveal microhomology preferences of 1–2 base pairs, differing from the smaller type 1 and type 2 deletions. These differential characteristics suggest the existence of molecularly distinct deletion pathways. Type 3 deletions are abundant in human tumors, can dominate the deletion landscape, and are associated with DNA damage response status and treatment modality. Conclusions Our data highlight the essential contribution of the DDT system to genome maintenance and type 3 deletions as mutational signature of replication stress. The unique characteristics of type 3 deletions implicate the existence of a novel deletion pathway in mice and humans that is counteracted by DDT. Graphical Abstract |
| format | Article |
| id | doaj-art-b67d91180f0e4dcb981bd36e0c862c82 |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-b67d91180f0e4dcb981bd36e0c862c822025-01-05T12:31:58ZengBMCGenome Biology1474-760X2024-12-0125112810.1186/s13059-024-03451-zMolecular dependencies and genomic consequences of a global DNA damage tolerance defectDaniel de Groot0Aldo Spanjaard1Ronak Shah2Maaike Kreft3Ben Morris4Cor Lieftink5Joyce J. I. Catsman6Shirley Ormel7Matilda Ayidah8Bas Pilzecker9Olimpia Alessandra Buoninfante10Paul C. M. van den Berk11Roderick L. Beijersbergen12Heinz Jacobs13Division of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer InstituteDivision of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteDivision of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer InstituteDivision of Tumor Biology & Immunology, The Netherlands Cancer InstituteAbstract Background DNA damage tolerance (DDT) enables replication to continue in the presence of fork stalling lesions. In mammalian cells, DDT is regulated by two independent pathways, controlled by the polymerase REV1 and ubiquitinated PCNA, respectively. Results To determine the molecular and genomic impact of a global DDT defect, we studied PcnaK164R/−;Rev1−/− compound mutants in mouse cells. Double-mutant cells display increased replication stress, hypersensitivity to genotoxic agents, replication speed, and repriming. A whole-genome CRISPR-Cas9 screen revealed a strict reliance of double-mutant cells on the CST complex, where CST promotes fork stability. Whole-genome sequencing indicated that this double-mutant DDT defect favors the generation of large, replication-stress inducible deletions of 0.4–4.0 kbp, defined as type 3 deletions. Junction break sites of these deletions reveal microhomology preferences of 1–2 base pairs, differing from the smaller type 1 and type 2 deletions. These differential characteristics suggest the existence of molecularly distinct deletion pathways. Type 3 deletions are abundant in human tumors, can dominate the deletion landscape, and are associated with DNA damage response status and treatment modality. Conclusions Our data highlight the essential contribution of the DDT system to genome maintenance and type 3 deletions as mutational signature of replication stress. The unique characteristics of type 3 deletions implicate the existence of a novel deletion pathway in mice and humans that is counteracted by DDT. Graphical Abstracthttps://doi.org/10.1186/s13059-024-03451-z |
| spellingShingle | Daniel de Groot Aldo Spanjaard Ronak Shah Maaike Kreft Ben Morris Cor Lieftink Joyce J. I. Catsman Shirley Ormel Matilda Ayidah Bas Pilzecker Olimpia Alessandra Buoninfante Paul C. M. van den Berk Roderick L. Beijersbergen Heinz Jacobs Molecular dependencies and genomic consequences of a global DNA damage tolerance defect Genome Biology |
| title | Molecular dependencies and genomic consequences of a global DNA damage tolerance defect |
| title_full | Molecular dependencies and genomic consequences of a global DNA damage tolerance defect |
| title_fullStr | Molecular dependencies and genomic consequences of a global DNA damage tolerance defect |
| title_full_unstemmed | Molecular dependencies and genomic consequences of a global DNA damage tolerance defect |
| title_short | Molecular dependencies and genomic consequences of a global DNA damage tolerance defect |
| title_sort | molecular dependencies and genomic consequences of a global dna damage tolerance defect |
| url | https://doi.org/10.1186/s13059-024-03451-z |
| work_keys_str_mv | AT danieldegroot moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT aldospanjaard moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT ronakshah moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT maaikekreft moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT benmorris moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT corlieftink moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT joycejicatsman moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT shirleyormel moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT matildaayidah moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT baspilzecker moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT olimpiaalessandrabuoninfante moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT paulcmvandenberk moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT rodericklbeijersbergen moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect AT heinzjacobs moleculardependenciesandgenomicconsequencesofaglobaldnadamagetolerancedefect |