Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a

Fields, Christopher J.; Lü, Li; Hiers, Nicholas M.; Li, Tianqi; Sheng, Peike; Huda, Taha I.; Shan, Jixiu; Gay, Lauren; Gu, Tongjun; Bian, Jiang; Kilberg, Michael S.; Renne, Rolf; Xie, Mingyi

doi:10.1371/journal.pgen.1009934

Cited by 12 publications

(9 citation statements)

References 105 publications

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“…Fig 12). Previous studies reported a correlation between the number of detected hybrids and the expression levels of its miRNA and mRNA components [15, 31]. These correlations hold true for our matching total and the small RNA-seq data when taking the total count across the replicates (Fig 4.B, left panels).…”

Section: Resultssupporting

confidence: 81%

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Gureghian

Herbst

Kozar

et al. 2023

Preprint

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Therapy Induced Senescence (TIS) leads to sustained growth arrest of cancer cells. Conversely, the Senescence Associated Secretory Phenotype (SASP) has been shown to promote tumorigenesis and metastasis. The associated cytostasis, which was first conceived as permanent, has since been shown to be reversible. Cells escaping senescence further enhance the aggressiveness of cancers. Despite all this, the mechanisms by which cancer cells escape senescence are poorly understood and the development of specific and efficient 'senolytics', specifically targeting senescent cancer cells, is in its infancy. Together with targeted therapeutics, senolytics constitute a promising avenue for improved cancer treatments. Understanding how cancer cells evade senescence is needed to optimize the clinical benefits of this promising approach. Here we characterized the response of three different NRAS mutant melanoma cell lines to a combination of CDK4/6 and MEK inhibitors over 33 days. Transcriptomic data show that all cell lines trigger a senescence program coupled with strong induction of interferons. Kinome profiling revealed the activation of Receptor Tyrosine Kinases (RTKs) and enriched downstream signaling of neurotrophin, ErbB and insulin pathways. Characterization of the miRNA interactome associates miR-211-5p with resistant phenotypes. Finally, integration of bulk and single-cell RNA-seq data identified biological processes perturbed during senescence establishment and escape, and predicts new genes involved in this shift. Overall, our data associate insulin signaling with persistence of a senescent phenotype and suggest a new role for interferon gamma in senescence escape through the induction of EMT and the activation of ERK5 signaling.

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Section: Resultssupporting

confidence: 81%

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Gureghian

Herbst

Kozar

et al. 2023

Preprint

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show abstract

“…After that, intermolecular ligation and libraries were generated as previously described 35 . Libraries were separated and size selected between 147 and 527 bp as previously described 37 . Three AGO1-CLASH libraries were generated from control-KO and Dora -KO S2 cells respectively.…”

Section: Methodsmentioning

confidence: 99%

A conserved sequence inDrosophilaArgonaute1 mRNA contributes to stress response via inducing miR-999 degradation

Sheng

et al. 2022

Preprint

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MicroRNAs (miRNAs) load onto Argonaute (AGO) proteins and target messenger RNAs (mRNA) to directly suppress gene expression at the post-transcriptional level. However, miRNA degradation can be triggered when there is extended base-pairing between miRNAs and the target RNAs. Such base-pairing can induce confirmational change of AGO and recruitment of ZSWIM8 ubiquitin ligase to mark AGO for proteasomal degradation, while the miRNAs are subsequently degraded. This target RNA-directed miRNA degradation (TDMD) mechanism appears to be an evolutionary conserved mechanism, but recent studies have focused on identifying endogenous TDMD events in the mammalian systems. Here, we performed AGO1-CLASH (crosslinking and sequencing of miRNA-mRNA hybrids) in Drosophila S2 cells, with Dora (ortholog of vertebrate ZSWIM8) knockout (KO) mediated by CRISPR-Cas9 to identify five TDMD triggers (sequences that can induce miRNA degradation). Interestingly, one trigger residing in the 3′ UTR of AGO1 mRNA induces miR-999 degradation. CRISPR-Cas9 KO of the AGO1 trigger in S2 cells and in Drosophila elevates miR-999 abundance, with concurrent repression of the miR-999 targets. AGO1 trigger-KO flies respond poorly to hydrogen peroxide-induced stress, demonstrating the physiological importance of a single TDMD event.

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“…After that, intermolecular ligation and libraries were generated as previously described 39 . Libraries were separated and size selected between 147 and 527 bp, as previously described 41 . Three AGO1-CLASH libraries were generated from control-KO and Dora-KO S2 cells, respectively.…”

Section: Ago1-clashmentioning

confidence: 99%

Screening of Drosophila microRNA-degradation sequences reveals Argonaute1 mRNA’s role in regulating miR-999

Sheng

et al. 2023

Nat Commun

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MicroRNAs (miRNA) load onto AGO proteins to target mRNAs for translational repression or degradation. However, miRNA degradation can be triggered when extensively base-paired with target RNAs, which induces confirmational change of AGO and recruitment of ZSWIM8 ubiquitin ligase to mark AGO for proteasomal degradation. This target RNA-directed miRNA degradation (TDMD) mechanism appears to be evolutionarily conserved, but recent studies have focused on mammalian systems. Here, we performed AGO1-CLASH in Drosophila S2 cells, with Dora (ortholog of vertebrate ZSWIM8) knockout mediated by CRISPR-Cas9 to identify five TDMD triggers (sequences that can induce miRNA degradation). Interestingly, one trigger in the 3′ UTR of AGO1 mRNA induces miR-999 degradation. CRISPR-Cas9 knockout of the AGO1 trigger in S2 cells and in Drosophila specifically elevates miR-999, with concurrent repression of the miR-999 targets. AGO1 trigger knockout flies respond poorly to hydrogen peroxide-induced stress, demonstrating the physiological importance of this TDMD event.

show abstract

Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a

Cited by 12 publications

References 105 publications

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

A conserved sequence inDrosophilaArgonaute1 mRNA contributes to stress response via inducing miR-999 degradation

Screening of Drosophila microRNA-degradation sequences reveals Argonaute1 mRNA’s role in regulating miR-999

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