Protein kinase RNA-activated (PKR) induces immune response by sensing viral double-stranded RNAs (dsRNAs). However, growing evidence suggests that PKR can also be activated by endogenously expressed dsRNAs. Here, we capture these dsRNAs by formaldehyde-mediated crosslinking and immunoprecipitation sequencing and find that various noncoding RNAs interact with PKR. Surprisingly, the majority of the PKR-interacting RNA repertoire is occupied by mitochondrial RNAs (mtRNAs). MtRNAs can form intermolecular dsRNAs owing to bidirectional transcription of the mitochondrial genome and regulate PKR and eIF2α phosphorylation to control cell signaling and translation. Moreover, PKR activation by mtRNAs is counteracted by PKR phosphatases, disruption of which causes apoptosis from PKR overactivation even in uninfected cells. Our work unveils dynamic regulation of PKR even without infection and establishes PKR as a sensor for nuclear and mitochondrial signaling cues in regulating cellular metabolism.

蛋白激酶RNA激活（PKR）通过感测病毒双链RNA（dsRNA）诱导免疫反应。但是，越来越多的证据表明，PKR也可以被内源表达的dsRNA激活。在这里，我们通过甲醛介导的交联和免疫沉淀测序捕获这些dsRNA，发现各种非编码RNA与PKR相互作用。令人惊讶的是，大多数与PKR相互作用的RNA都被线粒体RNA（mtRNA）占据。由于线粒体基因组的双向转录，MtRNA可以形成分子间dsRNA，并调节PKR和eIF2α磷酸化来控制细胞信号转导和翻译。此外，由mtR激活的PKR被PKR磷酸酶所抵消，即使在未感染的细胞中，PKR磷酸酶的破坏也会引起PKR过度激活引起的细胞凋亡。