PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator

Kim, Yoosik; Lee, Jung Hyun; Park, Jong-Eun; Cho, Jun; Yi, Hyerim; Kim, V. Narry

doi:10.1101/gad.242644.114

Cited by 122 publications

(137 citation statements)

References 62 publications

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“…2A); at present, it is entirely unclear how this might occur. A recent study showed that PKR is activated by inverted Alu repeats when these factors mix as the nuclear envelope breaks down during mitosis (29). PA has been shown to induce mitosis (30), and we considered whether mitosis could trigger a snoRNA-PKR interaction.…”

Section: Discussionmentioning

confidence: 99%

Potential role for snoRNAs in PKR activation during metabolic stress

Youssef

Safran

Nakamura

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

106

103

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Protein kinase RNA-activated (PKR) has long been known to be activated by viral double-stranded RNA (dsRNA) as part of the mammalian immune response. However, in mice PKR is also activated by metabolic stress in the absence of viral infection, and this requires a functional kinase domain, as well as a functional dsRNA-binding domain. The endogenous cellular RNA that potentially leads to PKR activation during metabolic stress is unknown. We investigated this question using mouse embryonic fibroblast cells expressing wild-type PKR (PKR WT ) or PKR with a point mutation in each dsRNA-binding motif (PKR RM ). Using this system, we identified endogenous RNA that interacts with PKR after induction of metabolic stress by palmitic acid (PA) treatment. Specifically, RIP-Seq analyses showed that the majority of enriched RNAs that interacted with WT PKR (≥twofold, false discovery rate ≤ 5%) were small nucleolar RNAs (snoRNAs). Immunoprecipitation of PKR in extracts of UV-cross-linked cells, followed by RT-qPCR, confirmed that snoRNAs were enriched in PKR WT samples after PA treatment, but not in the PKR RM samples. We also demonstrated that a subset of identified snoRNAs bind and activate PKR in vitro; the presence of a 5′-triphosphate enhanced PKR activity compared with the activity with a 5′-monophosphate, for some, but not all, snoRNAs. Finally, we demonstrated PKR activation in cells upon snoRNA transfection, supporting our hypothesis that endogenous snoRNAs can activate PKR. Our results suggest an unprecedented and unexpected model whereby snoRNAs play a role in the activation of PKR under metabolic stress.PKR | snoRNA | metabolic stress | phosphorylation | RNA-binding protein

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Section: Discussionmentioning

confidence: 99%

Potential role for snoRNAs in PKR activation during metabolic stress

Youssef

Safran

Nakamura

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

106

103

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“…One or both of these mechanisms could act upon mRNAs with EERs in their 3 ′ UTRs. In fact, PKR is activated by certain cellular dsRNAs only during mitosis, when the nuclear envelope is not present (Kim et al 2014), suggesting the presence of dsRNA in the cytoplasm might be dependent on cell cycle.…”

Section: Comparison Of Eer Data Sets With Data Sets Of Related Studiesmentioning

confidence: 99%

“…Recent studies reveal that cellular dsRNAs are capable of activating innate immune signaling pathways under various conditions (Nakamura et al 2010;Kim et al 2014). We were curious whether the expression of EERs could be regulated under conditions of stress, for example, during infection.…”

Section: Subsets Of Eers Are Differentially Expressed During Stress Amentioning

confidence: 99%

“…For instance, in human cells, endogenous dsRNA formed by pairing of inverted Alu repeats is released from the nucleus during mitosis to activate the dsRNA-binding protein PKR, and repress translation (Kim et al 2014). In a potentially related example, elevated levels of endogenous, repetitive Alu RNA, resulting from Dicer deficiency, leads to noncanonical activation of the NLRP3 inflammasome via MyD88 signaling (Tarallo et al 2012;Kerur et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide profiling of the C. elegans dsRNAome

Whipple

Youssef

Aruscavage

et al. 2015

RNA

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Recent studies hint that endogenous dsRNA plays an unexpected role in cellular signaling. However, a complete understanding of endogenous dsRNA signaling is hindered by an incomplete annotation of dsRNA-producing genes. To identify dsRNAs expressed in Caenorhabditis elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered RNA editing sites, which are strictly limited to long dsRNA substrates of Adenosine Deaminases that act on RNA (ADAR). We compared two alignment algorithms for mapping both unique and repetitive reads and detected as many as 664 editing-enriched regions (EERs) indicative of dsRNA loci. EERs are visually enriched on the distal arms of autosomes and are predicted to possess strong internal secondary structures as well as sequence complementarity with other EERs, indicative of both intramolecular and intermolecular duplexes. Most EERs were associated with protein-coding genes, with ∼1.7% of all C. elegans mRNAs containing an EER, located primarily in very long introns and in annotated, as well as unannotated, 3 ′ UTRs. In addition to numerous EERs associated with coding genes, we identified a population of prospective noncoding EERs that were distant from protein-coding genes and that had little or no coding potential. Finally, subsets of EERs are differentially expressed during development as well as during starvation and infection with bacterial or fungal pathogens. By combining RNA-seq with freely available bioinformatics tools, our workflow provides an easily accessible approach for the identification of dsRNAs, and more importantly, a catalog of the C. elegans dsRNAome.

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“…′ UTR IRAlus have the potential to bind and activate another dsRNA-binding protein, the translational inhibitor protein kinase R (PKR), making 3 ′ UTR IRAlus negative regulators of mRNA translation both in cis and in trans (Elbarbary et al 2013;Kim et al 2014). STAU1 also competes with PKR for binding to 3 ′ UTR IRAlus so as to alleviate translational repression (Elbarbary et al 2013).…”

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confidence: 99%

CARMing down the SINEs of anarchy: two paths to freedom from paraspeckle detention

Elbarbary

Maquat

2015

Genes Dev.

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A subset of messenger RNAs (mRNAs) that contain inverted Alu elements in their 3′ untranslated region are inefficiently exported to the cytoplasm and retained in subnuclear bodies called paraspeckles. The arginine methyltransferase CARM1 (coactivator-associated arginine methyltransferase 1) promotes the nuclear export of these mRNAs by methylating the paraspeckle component p54nrb, which reduces the binding of p54nrb to the inverted Alu elements, and down-regulating synthesis of another paraspeckle component, the long noncoding RNA NEAT1, which inhibits paraspeckle formation.

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PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator

Cited by 122 publications

References 62 publications

Potential role for snoRNAs in PKR activation during metabolic stress

Potential role for snoRNAs in PKR activation during metabolic stress

Genome-wide profiling of the C. elegans dsRNAome

CARMing down the SINEs of anarchy: two paths to freedom from paraspeckle detention

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