Dynamic Nature of Cleavage Bodies and Their Spatial Relationship to DDX1 Bodies, Cajal Bodies, and Gems

Li, Lei; Roy, K C; Katyal, Sachin; Sun, Xuejun; Bléoo, Stacey; Godbout, Roseline

doi:10.1091/mbc.e05-08-0768

Cited by 56 publications

(49 citation statements)

References 62 publications

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“…S5 in the supplemental material), suggesting that the reduced numbers of RPA foci observed upon DDX1 depletion following IR treatment are unlikely to be due to a role for DDX1 in replication. In agreement with this, we have previously shown that DDX1 does not form foci in cells treated with aphidicolin, cisplatin, or UV until 24 h posttreatment, when stalled replication forks eventually collapse and form DSBs (9,24).…”

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

confidence: 84%

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

Germain

Poon

et al. 2016

Molecular and Cellular Biology

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133

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

confidence: 84%

“…First, DNA replication stress, shown by others to induce R-loop formation (64,65), did not result in accumulation of DDX1 at chromatin (9,24). However, DDX1 foci were observed 24 h after replication disruption, when stalled replication forks eventually collapse and form DSBs.…”

Section: Discussionmentioning

confidence: 92%

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

Germain

Poon

et al. 2016

Molecular and Cellular Biology

Self Cite

133

138

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“…DDX1, a helicase involved in transcription, 53,54 mRNA processing 55,56 and translation, 57 is upregulated in neuroblastoma and retinoblastoma cell lines and tumors.…”

Section: Cancer and Agingmentioning

confidence: 99%

“…In the human host, DDX1 (Fig. 4) functions in transcription, 53,54 premRNA processing 55,56 and mRNA translation. 57 It interacts with the oligomerization domain of HIV-1 Rev, 58 and promotes Revoligomerization on the RRE.…”

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confidence: 99%

RNA helicases in infection and disease

Steimer

Klostermeier

2012

RNA Biology

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“…This is reminiscent of the relationship between gems, Cajal bodies and cleavage bodies, all structures involved in steps of pre-mRNA processing. These bodies can occur as separate nuclear structures, but can be also be twinned or colocalised in some situations (Li et al, 2006). Intriguingly, given the spatial juxtaposition of KAKA foci and PML-NBs, both KAP1 and PML are proteins of the RBCC family.…”

Section: Krab Zfps Characterise a Novel Nuclear Bodymentioning

confidence: 99%

KRAB zinc-finger proteins localise to novel KAP1-containing foci that are adjacent to PML nuclear bodies

Briers

Crawford

Bickmore

et al. 2009

Journal of Cell Science

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The KRAB-zinc finger proteins (KRAB-ZFPs) represent a very large, but poorly understood, family of transcriptional regulators in mammals. They are thought to repress transcription via their interaction with KRAB-associated protein 1 (KAP1), which then assembles a complex of chromatin modifiers to lay down histone marks that are associated with inactive chromatin. Studies of KRAB-ZFP/KAP1-mediated gene silencing, using reporter constructs and ectopically expressed proteins, have shown colocalisation of both KAP1 and repressed reporter target genes to domains of constitutive heterochromatin in the nucleus. However, we show here that although KAP1 does indeed become recruited to pericentric heterochromatin during differentiation of mouse embryonic stem (ES) cells, endogenous KRAB-ZFPs do not. Rather, KRAB-ZFPs and KAP1 relocalise to novel nucleoplasmic foci that we have termed KRAB- and KAP1-associated (KAKA) foci. HP1s can also concentrate in these foci and there is a close spatial relationship between KAKA nuclear foci and PML nuclear bodies. Finally, we reveal differential requirements for the recruitment of KAP1 to pericentric heterochromatin and KAKA foci, and suggest that KAKA foci may contain sumoylated KAP1 – the form of the protein that is active in transcriptional repression.

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Dynamic Nature of Cleavage Bodies and Their Spatial Relationship to DDX1 Bodies, Cajal Bodies, and Gems

Cited by 56 publications

References 62 publications

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

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

RNA helicases in infection and disease

KRAB zinc-finger proteins localise to novel KAP1-containing foci that are adjacent to PML nuclear bodies

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