RNA transcripts serve as a template for double-strand break repair in human cells
Abstract Double-strand breaks (DSBs) are toxic lesions that lead to genome instability. While canonical DSB repair pathways typically operate independently of RNA, growing evidence suggests that RNA:DNA hybrids and nearby transcripts can influence repair outcomes. However, whether transcript RNA can...
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| Language: | English |
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-59510-x |
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| author | Manisha Jalan Alessandra Brambati Hina Shah Niamh McDermott Juber Patel Yingjie Zhu Ahmet Doymaz Julius Wu Kyrie S. Anderson Andrea Gazzo Fresia Pareja Takafumi N. Yamaguchi Theodore Vougiouklakis Sana Ahmed-Seghir Philippa Steinberg Anna Neiman-Golden Benura Azeroglu Joan Gomez-Aguilar Edaise M. da Silva Suleman Hussain Daniel Higginson Paul C. Boutros Nadeem Riaz Jorge S. Reis-Filho Simon N. Powell Agnel Sfeir |
| author_facet | Manisha Jalan Alessandra Brambati Hina Shah Niamh McDermott Juber Patel Yingjie Zhu Ahmet Doymaz Julius Wu Kyrie S. Anderson Andrea Gazzo Fresia Pareja Takafumi N. Yamaguchi Theodore Vougiouklakis Sana Ahmed-Seghir Philippa Steinberg Anna Neiman-Golden Benura Azeroglu Joan Gomez-Aguilar Edaise M. da Silva Suleman Hussain Daniel Higginson Paul C. Boutros Nadeem Riaz Jorge S. Reis-Filho Simon N. Powell Agnel Sfeir |
| author_sort | Manisha Jalan |
| collection | DOAJ |
| description | Abstract Double-strand breaks (DSBs) are toxic lesions that lead to genome instability. While canonical DSB repair pathways typically operate independently of RNA, growing evidence suggests that RNA:DNA hybrids and nearby transcripts can influence repair outcomes. However, whether transcript RNA can directly serve as a template for DSB repair in human cells remains unclear. In this study, we develop fluorescence and sequencing-based assays to show that RNA-containing oligonucleotides and messenger RNA can serve as templates during DSB repair. We conduct a CRISPR/Cas9-based genetic screen to identify factors that promote RNA-templated DSB repair (RT-DSBR). Of the candidate polymerases, we identify DNA polymerase zeta (Polζ) as a potential reverse transcriptase that facilitates RT-DSBR. Furthermore, analysis of cancer genome sequencing data reveals whole intron deletions - a distinct genomic signature of RT-DSBR that occurs when spliced mRNA guides repair. Altogether, our findings highlight RT-DSBR as an alternative pathway for repairing DSBs in transcribed genes, with potential mutagenic consequences. |
| format | Article |
| id | doaj-art-b26f5d46ee024eacba7094f2bd77fac6 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-b26f5d46ee024eacba7094f2bd77fac62025-08-20T03:53:12ZengNature PortfolioNature Communications2041-17232025-05-0116111610.1038/s41467-025-59510-xRNA transcripts serve as a template for double-strand break repair in human cellsManisha Jalan0Alessandra Brambati1Hina Shah2Niamh McDermott3Juber Patel4Yingjie Zhu5Ahmet Doymaz6Julius Wu7Kyrie S. Anderson8Andrea Gazzo9Fresia Pareja10Takafumi N. Yamaguchi11Theodore Vougiouklakis12Sana Ahmed-Seghir13Philippa Steinberg14Anna Neiman-Golden15Benura Azeroglu16Joan Gomez-Aguilar17Edaise M. da Silva18Suleman Hussain19Daniel Higginson20Paul C. Boutros21Nadeem Riaz22Jorge S. Reis-Filho23Simon N. Powell24Agnel Sfeir25Department of Radiation Oncology, Memorial Sloan Kettering Cancer CenterMolecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterMolecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer CenterDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer CenterDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer CenterMolecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterMolecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer CenterDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer CenterDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer CenterDepartment of Human Genetics, University of CaliforniaDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer CenterDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer CenterDepartment of Human Genetics, University of CaliforniaDepartment of Human Genetics, University of CaliforniaLaboratory of Genome Integrity, National Cancer Institute (NCI), National Institutes of Health (NIH)Department of Radiation Oncology, Memorial Sloan Kettering Cancer CenterDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer CenterDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer CenterDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer CenterDepartment of Human Genetics, University of CaliforniaDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer CenterDepartment of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer CenterDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer CenterMolecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterAbstract Double-strand breaks (DSBs) are toxic lesions that lead to genome instability. While canonical DSB repair pathways typically operate independently of RNA, growing evidence suggests that RNA:DNA hybrids and nearby transcripts can influence repair outcomes. However, whether transcript RNA can directly serve as a template for DSB repair in human cells remains unclear. In this study, we develop fluorescence and sequencing-based assays to show that RNA-containing oligonucleotides and messenger RNA can serve as templates during DSB repair. We conduct a CRISPR/Cas9-based genetic screen to identify factors that promote RNA-templated DSB repair (RT-DSBR). Of the candidate polymerases, we identify DNA polymerase zeta (Polζ) as a potential reverse transcriptase that facilitates RT-DSBR. Furthermore, analysis of cancer genome sequencing data reveals whole intron deletions - a distinct genomic signature of RT-DSBR that occurs when spliced mRNA guides repair. Altogether, our findings highlight RT-DSBR as an alternative pathway for repairing DSBs in transcribed genes, with potential mutagenic consequences.https://doi.org/10.1038/s41467-025-59510-x |
| spellingShingle | Manisha Jalan Alessandra Brambati Hina Shah Niamh McDermott Juber Patel Yingjie Zhu Ahmet Doymaz Julius Wu Kyrie S. Anderson Andrea Gazzo Fresia Pareja Takafumi N. Yamaguchi Theodore Vougiouklakis Sana Ahmed-Seghir Philippa Steinberg Anna Neiman-Golden Benura Azeroglu Joan Gomez-Aguilar Edaise M. da Silva Suleman Hussain Daniel Higginson Paul C. Boutros Nadeem Riaz Jorge S. Reis-Filho Simon N. Powell Agnel Sfeir RNA transcripts serve as a template for double-strand break repair in human cells Nature Communications |
| title | RNA transcripts serve as a template for double-strand break repair in human cells |
| title_full | RNA transcripts serve as a template for double-strand break repair in human cells |
| title_fullStr | RNA transcripts serve as a template for double-strand break repair in human cells |
| title_full_unstemmed | RNA transcripts serve as a template for double-strand break repair in human cells |
| title_short | RNA transcripts serve as a template for double-strand break repair in human cells |
| title_sort | rna transcripts serve as a template for double strand break repair in human cells |
| url | https://doi.org/10.1038/s41467-025-59510-x |
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