Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing

Yoon, J.-H.; Min, K.-W.; Jo, M. H.; Song, M.; Ko, S.; Lee, J. W.; Shim, M. J.; Kim, K.; Park, H. B.; Ha, S.; Mun, H.; Polash, A.; Hafner, M.; Cho, J.-H.; Kim, D.-S.; Hohng, S.; Kang, S.-U.

doi:10.1101/2023.03.15.532749

bioRxiv · 10.1101/2023.03.15.532749

Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing

Yoon, J.-H.·Min, K.-W.·Jo, M. H.·Song, M.·Ko, S.·Lee, J. W.·Shim, M. J.·Kim, K.·Park, H. B.·Ha, S.·Mun, H.·Polash, A.·Hafner, M.·Cho, J.-H.·Kim, D.-S.·Hohng, S.·Kang, S.-U.

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Abstract

Although Argonaute (AGO) proteins have been the focus of microRNA (miRNA) studies, we observed AGO-free mature miRNAs directly interacting with RNA-binding proteins, implying the sophisticated nature of fine-tuning gene regulation by miRNAs. To investigate microRNA-binding proteins (miRBPs) globally, we analyzed PAR-CLIP data sets to identify RBP quaking (QKI) as a novel miRBP for let-7b. Potential existence of AGO-free miRNAs were further verified in genetically engineered AGO-depleted human and mouse cells. We have shown that QKI serves as an auxiliary factor empowering AGO2/let-7b-mediated gene silencing. Depletion of QKI decreases interaction of AGO2 with let-7b and target mRNA, consequently controlling target mRNA decay. QKI, however, also suppresses the dissociation of let-7b from AGO2, and slows assembly of AGO2/miRNA/target mRNA complexes at the single-molecule level. We also revealed that QKI suppresses cMYC expression at post-transcriptional level, and decreases proliferation and migration of HeLa cells, demonstrating that QKI is a tumor suppressor gene by in part augmenting let-7b activity. Our data show that QKI is a new type of RBP implicated in the versatile regulation of miRNA-mediated gene silencing.

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Yoon, J.-H., Min, K.-W., Jo, M. H., Song, M., Ko, S., Lee, J. W., Shim, M. J., Kim, K., Park, H. B., Ha, S., Mun, H., Polash, A., Hafner, M., Cho, J.-H., Kim, D.-S., Hohng, S., Kang, S.-U.. 2023-03-15. Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing. https://doi.org/10.1101/2023.03.15.532749

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