Synapse - RNA transcripts serve as a template for double-strand break repair in human cells

RNA transcripts serve as a template for double-strand break repair in human cells Journal Article

Authors:	Jalan, M.; Brambati, A.; Shah, H.; McDermott, N.; Patel, J.; Zhu, Y.; Doymaz, A.; Wu, J.; Anderson, K. S.; Gazzo, A.; Pareja, F.; Yamaguchi, T. N.; Vougiouklakis, T.; Ahmed-Seghir, S.; Steinberg, P.; Neiman-Golden, A.; Azeroglu, B.; Gomez-Aguilar, J.; da Silva, E. M.; Hussain, S.; Higginson, D.; Boutros, P. C.; Riaz, N.; Reis-Filho, J. S.; Powell, S. N.; Sfeir, A.
Article Title:	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 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. © The Author(s) 2025.
Keywords:	controlled study; unclassified drug; human cell; major clinical study; exon; genetics; nonhuman; flow cytometry; dna polymerase; genetic analysis; quality control; metabolism; dna repair; fluorescence; genotype; intron; enzyme activity; simulation; rna; dna; algorithm; messenger rna; rna, messenger; probability; gene disruption; genomic instability; amplicon; western blotting; dna breaks, double-stranded; double stranded dna break; genome; codon; oligonucleotide; fluorescence activated cell sorting; genotyping; dna-directed dna polymerase; dna template; dna directed dna polymerase; templates, genetic; translesion synthesis; gene insertion sequence; reverse transcription; high throughput sequencing; double strand break repair; rna directed dna polymerase; sanger sequencing; cell component; cancer; humans; human; article; rna sequencing; crispr cas system; droplet digital polymerase chain reaction; crispr-cas systems; crispr-cas9 system; dna polymerase zeta; long interspersed nuclear element 1; dna contamination; random mutagenesis
Journal Title:	Nature Communications
Volume:	16
ISSN:	2041-1723
Publisher:	Nature Publishing Group
Date Published:	2025-05-10
Start Page:	4349
Language:	English
DOI:	10.1038/s41467-025-59510-x
PUBMED:	40348775
PROVIDER:	scopus
PMCID:	PMC12065846
DOI/URL:	https://www.scopus.com/inward/record.uri?eid=2-s2.0-105004688097&doi=10.1038%2fs41467-025-59510-x&partnerID=40&md5=9791df0ad50e9118038f190128fb4d66
Notes:	Article -- MSK Cancer Center Support Grant (P30 CA008748) acknowledged in PubMed and PDF -- MSK corresponding authors are Simon Powell and Agnel Sfeir -- Source: Scopus