A small RNA response at DNA ends in Drosophila

Michalik, Katharina; Böttcher, Romy; Förstemann, Klaus

doi:10.1093/nar/gks711

Cited by 128 publications

(167 citation statements)

References 39 publications

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“…This model also implies that diRISCs recruit DSB repair factors to the target DSB sites. Similar small RNAs induced by DDR have been reported in other systems [7][8][9]. However, the specific function of small RNAs has remained largely unknown.…”

supporting

confidence: 69%

diRNA-Ago2-RAD51 complexes at double-strand break sites

Yamanaka

Siomi

2014

Cell Res

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supporting

confidence: 69%

diRNA-Ago2-RAD51 complexes at double-strand break sites

Yamanaka

Siomi

2014

Cell Res

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“…By using a relatively short sequence that is homologous only to the upstream region of the I-SceI site, we avoided this possible scenario. Second, recent studies have shown that small noncoding RNAs are induced at DSBs (50)(51)(52). These small RNAs are transcribed in both orientations and are preferentially generated in the upstream vicinity of DSBs (51,52).…”

Section: Ddx1 Contributes To Dsb Repair and Cell Survival Post-irmentioning

confidence: 99%

DEAD Box 1 Facilitates Removal of RNA and Homologous Recombination at DNA Double-Strand Breaks

Germain

Poon

et al. 2016

Molecular and Cellular Biology

130

138

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Although RNA and RNA-binding proteins have been linked to double-strand breaks (DSBs), little is known regarding their roles in the cellular response to DSBs and, if any, in the repair process. Here, we provide direct evidence for the presence of RNA-DNA hybrids at DSBs and suggest that binding of RNA to DNA at DSBs may impact repair efficiency. Our data indicate that the RNAunwinding protein DEAD box 1 (DDX1) is required for efficient DSB repair and cell survival after ionizing radiation (IR), with depletion of DDX1 resulting in reduced DSB repair by homologous recombination (HR). While DDX1 is not essential for end resection, a key step in homology-directed DSB repair, DDX1 is required for maintenance of the single-stranded DNA once generated by end resection. We show that transcription deregulation has a significant effect on DSB repair by HR in DDX1-depleted cells and that RNA-DNA duplexes are elevated at DSBs in DDX1-depleted cells. Based on our combined data, we propose a role for DDX1 in resolving RNA-DNA structures that accumulate at DSBs located at sites of active transcription. Our findings point to a previously uncharacterized requirement for clearing RNA at DSBs for efficient repair by HR. DEAD box proteins are a family of putative RNA helicases that function by altering RNA secondary structure. This protein family has been implicated in all aspects of RNA metabolism. The DEAD box 1 gene (DDX1) is a widely expressed gene that is misexpressed in a number of cancers, including retinoblastoma, neuroblastoma, and breast cancer (1, 2). Knockout of DDX1 leads to early embryonic lethality in mice and severely reduced fertility in flies (3, 4). DDX1 is involved in the transport of RNAs from the nucleus to the cytoplasm and regulates cytoplasmic localization of the splicing-regulatory protein KSRP (5). In neurons, DDX1 resides in RNA-transporting granules, cytoplasmic organelles that regulate the localization and expression of target mRNAs (6, 7). DDX1 has also been identified as a core subunit of the human tRNA ligase complex which is essential for tRNA splicing (8).In addition to its roles in RNA metabolism, DDX1 has been implicated in the cellular response to DNA double-strand breaks (DSBs). Upon treatment of cells with ionizing radiation (IR), DDX1 rapidly accumulates at a subset of DNA DSBs (ϳ30%), where it forms IR-induced foci that colocalize with ␥-H2AX, a marker for DSBs (9). DDX1 coimmunoprecipitates with the MRN (MRE11-RAD50-NBS1) complex, the early sensor of DNA DSBs, and ATM (ataxia telangiectasia mutated) protein, the key transducer of the signaling cascade in response to DSBs (10, 11). DSBs induce DDX1 phosphorylation in an ATM-dependent manner. Notably, IR-induced DDX1 foci are lost when cells are treated with RNase H, an enzyme that specifically digests RNA from RNA-DNA hybrids (9). These results suggest that RNA-DNA double-stranded structures are required for the presence and/or retention of DDX1 at DSBs. In line with this observation, biochemical analysis has shown that DDX1 can unwind both...

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“…Alternatively, phenotypic differences could be related to functions of AGO1 other than miRNA target repression. Indeed, the implication of AGO proteins in several pathways such as nonsense-mediated mRNA decay (Choe et al, 2010), alternative splicing (AmeyarZazoua et al, 2012;Yang et al, 2012b;Taliaferro et al, 2013;Alló et al, 2014), DNA double-strand break repair (Michalik et al, 2012;Wei et al, 2012), nucleosome occupancy at transcription start sites (Carissimi et al, 2015), and quality control of mRNAs encoding proteins entering the secretory pathway (Karamyshev et al, 2014) has been proposed during the last years. If that is the case, the conditional slicer-deficient alleles might be a valuable tool to investigate novel functions of plant AGO1 by decoupling these from target regulation.…”

Section: Slicer Activity In Mirna Biogenesis and Accumulationmentioning

confidence: 99%