R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability

• Published in: Nature communications Vol. 12; no. 1; pp. 7314 - 17
• Main Authors: Mosler, Thorsten, Conte, Francesca, Longo, Gabriel M. C., Mikicic, Ivan, Kreim, Nastasja, Möckel, Martin M., Petrosino, Giuseppe, Flach, Johanna, Barau, Joan, Luke, Brian, Roukos, Vassilis, Beli, Petra
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16.12.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 13/31; 14; 14/19; 38; 45; 631/337/1427; 631/337/475; 82/58; 96; Accumulation; Acute myeloid leukemia; Adult; Cell Line, Tumor; DEAD-box RNA Helicases - genetics; DEAD-box RNA Helicases - metabolism; Deoxyribonucleic acid; DNA; DNA - metabolism; DNA Breaks, Double-Stranded; DNA damage; Gene Knockdown Techniques; Genes, Tumor Suppressor; Genomic Instability; Genomics; HEK293 Cells; Humanities and Social Sciences; Humans; Hybrids; Inflammation; Inflammatory response; Leukemia; Leukemia, Myeloid, Acute; Mass spectrometry; Mass spectroscopy; multidisciplinary; Mutation; Myeloid leukemia; Nucleic Acid Conformation; Nucleic Acid Hybridization; Nucleic acids; Promoter Regions, Genetic; Promoters; Proteomes; Proteomics; R-Loop Structures - genetics; R-loops; Replication; Replication forks; Ribonucleic acid; RNA; RNA - metabolism; Science; Science (multidisciplinary); Stability; Transcription; Transcription, Genetic; Transcriptomes; Tumor suppressor genes; Tumors
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-27530-y

Transcription poses a threat to genomic stability through the formation of R-loops that can obstruct progression of replication forks. R-loops are three-stranded nucleic acid structures formed by an RNA–DNA hybrid with a displaced non-template DNA strand. We developed RNA–DNA Proximity Proteomics to map the R-loop proximal proteome of human cells using quantitative mass spectrometry. We implicate different cellular proteins in R-loop regulation and identify a role of the tumor suppressor DDX41 in opposing R-loop and double strand DNA break accumulation in promoters. DDX41 is enriched in promoter regions in vivo, and can unwind RNA–DNA hybrids in vitro. R-loop accumulation upon loss of DDX41 is accompanied with replication stress, an increase in the formation of double strand DNA breaks and transcriptome changes associated with the inflammatory response. Germline loss-of-function mutations in DDX41 lead to predisposition to acute myeloid leukemia in adulthood. We propose that R-loop accumulation and genomic instability-associated inflammatory response may contribute to the development of familial AML with mutated DDX41. Transcription can pose a threat to genomic instability through the formation of R-loops, which are RNA–DNA hybrids with a displaced non-template DNA strand. Here the authors mapped the R-loop proximal proteome in human cells and identified a role of the tumor suppressor DDX41 in opposing R-loop and double strand DNA break accumulation in gene promoters.