RNA transcripts serve as a template for double-strand break repair in human cells
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.
Authors
- Fresia Pareja (ORCID: https://orcid.org/0000-0003-3748-8049)
- Kyrie S Anderson
- Suleman S. Hussain (ORCID: https://orcid.org/0000-0003-1342-143X)
- Paul C. Boutros (ORCID: https://orcid.org/0000-0003-0553-7520)
- Philippa Steinberg (ORCID: https://orcid.org/0000-0002-2127-2692)
- Ahmet Doymaz (ORCID: https://orcid.org/0000-0003-4485-2742)
- Manisha Jalan (ORCID: https://orcid.org/0000-0002-4467-4934)
- Alessandra Brambati (ORCID: https://orcid.org/0000-0002-3816-425X)
- Nadeem Riaz (ORCID: https://orcid.org/0000-0001-9873-5862)
- Takafumi N. Yamaguchi (ORCID: https://orcid.org/0000-0003-1082-3871)
- Andrea Gazzo (ORCID: https://orcid.org/0009-0009-9282-4667)
- Edaise M. da Silva (ORCID: https://orcid.org/0000-0003-3281-7333)
- Agnel J. Sfeir (ORCID: https://orcid.org/0000-0003-1633-8535)
- Jing Wu (ORCID: https://orcid.org/0000-0003-2013-2863)
- Simon N. Powell (ORCID: https://orcid.org/0000-0002-8183-4765)
- Juber Patel (ORCID: https://orcid.org/0000-0003-1299-0083)
- Daniel S. Higginson (ORCID: https://orcid.org/0000-0002-6686-7454)
- Theodore Vougiouklakis (ORCID: https://orcid.org/0000-0001-8653-5679)
- Niamh McDermott (ORCID: https://orcid.org/0000-0001-6045-9364)
- Sana Ahmed‐Seghir
- Benura Azeroglu (ORCID: https://orcid.org/0000-0001-7243-384X)
- Hamza Shah (ORCID: https://orcid.org/0009-0007-7252-657X)
- Anna Neiman-Golden
- Yingjie Zhu (ORCID: https://orcid.org/0000-0003-1849-6019)
- Joan Gomez-Aguilar
- Jorge S. Reis-Filho
Institutions
- National Institutes of Health (US)
- Memorial Sloan Kettering Cancer Center (US)
- University of California, Los Angeles (US)
- SUNY Downstate Health Sciences University (US)
- Cornell University (US)
- Kettering University (US)
- National Cancer Institute (US)
- Broad Center (US)
- AstraZeneca (United States) (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-05-10
- DOI
- https://doi.org/10.1038/s41467-025-59510-x
- Citations
- 7
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 5.64
Funders
- Breast Cancer Research Foundation
- Susan G. Komen
- Swim Across America
- Cycle for Survival
- National Institutes of Health
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology
- National Cancer Institute