Work

RNase H-sensitive accumulation of APOBEC3B in a nucleolus after DNA damage

Year: 2025

Type: article

Abstract: Apolipoprotein B mRNA editing catalytic subunit 3B (A3B), a nuclear enzyme that catalyzes cytidine-to-uridine (C-to-U) editing in single-stranded DNA (ssDNA), contributes to genetic diversity in many cancers. A3B is induced or activated by DNA damage owing to a variety of factors; however, the mechanisms by which A3B accesses ssDNA within the genome remain unclear. In this study, we showed that in unstimulated cells, A3B is retained in the nucleoplasm in an RNA-dependent manner. Upon DNA damage induced by camptothecin or actinomycin D (Act D), both targeting topoisomerase I, or by 1-methyl-3-nitro-1-nitrosoguanidine (MNNG), an alkylating agent that generates apurinic/apyrimidinic sites, A3B accumulates at the nucleolar rim and interior. Using confocal microscopy, we assessed the colocalization of A3B with drug-induced R-loops. A3B accumulation was abolished by RNase H treatment, implicating R-loops in its localization. However, the S9.6 antibody, commonly used to detect DNA/RNA hybrids, did not identify R-loop-specific signals in the nucleolus, leaving the direct involvement of R-loops in A3B accumulation unresolved. Conversely, immunoprecipitation-mass spectrometry with data-independent acquisition (IP-MS DIA) revealed increased interactions between A3B and RNA helicases such as DDX17 and DDX21, which are known R-loop-binding proteins, following MNNG or Act D treatment. Our results demonstrate that A3B-induced secondary DNA damage occurs in the nucleolus after DNA damage, providing new insights into the acquisition of cancer diversity involving A3B and the DNA damage response in the nucleolus.

Source: Bioscience Reports

DOI: 10.1042/bsr20253880

Authors: Yohei Saito, Yumi Yamamoto, Fumihiko Yamamoto

Institution: Tohoku Medical and Pharmaceutical University

Language: English

Topic: RNA regulation and disease

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $1,960