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Exploring MicroRNAs on NIX-Dependent Mitophagy

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Book cover Mitophagy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1759))

Abstract

The dysregulation of autophagy is implicated in many pathological disorders including infections, aging, neurodegenerative diseases, and cancer. Autophagy can be precisely controlled both transcriptionally and translationally. Accumulating evidences show that the autophagy response is regulated by microRNAs, which therefore becomes subject area of interest in recent years. Herein, we give a brief introduction of the recent advancement in the regulation of microRNA on autophagy, and then we focus on the microRNA regulation of the mitophagy receptor, NIX. Finally, we present the methodology on how to study it in detail.

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References

  1. Aoki Y, Kanki T, Hirota Y, Kurihara Y, Saigusa T, Uchiumi T, Kang D (2011) Phosphorylation of Serine 114 on Atg32 mediates mitophagy. Mol Biol Cell 22(17):3206–3217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Barde I, Rauwel B, Marin-Florez RM, Corsinotti A, Laurenti E, Verp S, Offner S, Marquis J, Kapopoulou A, Vanicek J, Trono D (2013) A KRAB/KAP1-miRNA cascade regulates erythropoiesis through stage-specific control of mitophagy. Science 340(6130):350–353

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Basak I, Patil KS, Alves G, Larsen JP, Moller SG (2016) microRNAs as neuroregulators, biomarkers and therapeutic agents in neurodegenerative diseases. Cell Mol Life Sci 73(4):811–827

    Article  CAS  PubMed  Google Scholar 

  5. Ding WX, Ni HM, Li M, Liao Y, Chen X, Stolz DB, Dorn GW 2nd, Yin XM (2010) NIX is critical to two distinct phases of mitophagy, reactive oxygen species-mediated autophagy induction and Parkin-ubiquitin-p62-mediated mitochondrial priming. J Biol Chem 285(36):27879–27890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Dwivedi SK, Mustafi SB, Mangala LS, Jiang D, Pradeep S, Rodriguez-Aguayo C, Ling H, Ivan C, Mukherjee P, Calin GA, Lopez-Berestein G, Sood AK, Bhattacharya R (2016) Therapeutic evaluation of microRNA-15a and microRNA-16 in ovarian cancer. Oncotarget 7(12):15093

    Article  PubMed  Google Scholar 

  7. Elmore SP, Qian T, Grissom SF, Lemasters JJ (2001) The mitochondrial permeability transition initiates autophagy in rat hepatocytes. FASEB J 15(12):2286–2287

    Article  CAS  Google Scholar 

  8. Gomes BC, Rueff J, Rodrigues AS (2016) MicroRNAs and Cancer Drug Resistance. Methods Mol Biol 1395:137–162

    Article  CAS  PubMed  Google Scholar 

  9. Gunaratne PH, Creighton CJ, Watson M, Tennakoon JB (2010) Large-scale integration of MicroRNA and gene expression data for identification of enriched microRNA-mRNA associations in biological systems. Methods Mol Biol 667:297–315

    Article  CAS  PubMed  Google Scholar 

  10. Li W, Zhang X, Zhuang H, Chen HG, Chen Y, Tian W, Wu W, Li Y, Wang S, Zhang L, Chen Y, Li L, Zhao B, Sui S, Hu Z, Feng D (2014) MicroRNA-137 is a novel hypoxia-responsive microRNA that inhibits mitophagy via regulation of two mitophagy receptors FUNDC1 and NIX. J Biol Chem 289(15):10691–10701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Lin SL, Chang DC, Lin CH, Ying SY, Leu D, Wu DT (2011) Regulation of somatic cell reprogramming through inducible mir-302 expression. Nucleic Acids Res 39(3):1054–1065

    Article  CAS  PubMed  Google Scholar 

  12. Liu H (2012) MicroRNAs in breast cancer initiation and progression. Cell Mol Life Sci 69(21):3587–3599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Liu L, Feng D, Chen G, Chen M, Zheng Q, Song P, Ma Q, Zhu C, Wang R, Qi W, Huang L, Xue P, Li B, Wang X, Jin H, Wang J, Yang F, Liu P, Zhu Y, Sui S, Chen Q (2012) Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nat Cell Biol 14(2):177–185

    Article  CAS  Google Scholar 

  14. Miyoshi N, Ishii H, Nagano H, Haraguchi N, Dewi DL, Kano Y, Nishikawa S, Tanemura M, Mimori K, Tanaka F, Saito T, Nishimura J, Takemasa I, Mizushima T, Ikeda M, Yamamoto H, Sekimoto M, Doki Y, Mori M (2011) Reprogramming of mouse and human cells to pluripotency using mature microRNAs. Cell Stem Cell 8(6):633–638

    Article  CAS  PubMed  Google Scholar 

  15. Mughal W, Nguyen L, Pustylnik S, da Silva Rosa SC, Piotrowski S, Chapman D, Du M, Alli NS, Grigull J, Halayko AJ, Aliani M, Topham MK, Epand RM, Hatch GM, Pereira TJ, Kereliuk S, McDermott JC, Rampitsch C, Dolinsky VW, Gordon JW (2015) A conserved MADS-box phosphorylation motif regulates differentiation and mitochondrial function in skeletal, cardiac, and smooth muscle cells. Cell Death Dis 6:e1944

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Okamoto K, Kondo-Okamoto N, Ohsumi Y (2009) Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy. Dev Cell 17(1):87–97

    Article  PubMed  Google Scholar 

  17. Olde Loohuis NF, Nadif Kasri N, Glennon JC, van Bokhoven H, Hebert SS, Kaplan BB, Martens GJ, Aschrafi A (2016) The schizophrenia risk gene MIR137 acts as a hippocampal gene network node orchestrating the expression of genes relevant to nervous system development and function. Prog Neuropsychopharmacol Biol Psychiatry 73:109

    Article  CAS  PubMed  Google Scholar 

  18. Pattingre S, Tassa A, Qu X, Garuti R, Liang XH, Mizushima N, Packer M, Schneider MD, Levine B (2005) Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Cell 122(6):927–939

    Article  CAS  PubMed  Google Scholar 

  19. Rebane A (2015) microRNA and Allergy. Adv Exp Med Biol 888:331–352

    Article  CAS  PubMed  Google Scholar 

  20. Sarkar FH, Li Y, Wang Z, Kong D, Ali S (2010) Implication of microRNAs in drug resistance for designing novel cancer therapy. Drug Resist Updat 13(3):57–66

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Schweers RL, Zhang J, Randall MS, Loyd MR, Li W, Dorsey FC, Kundu M, Opferman JT, Cleveland JL, Miller JL, Ney PA (2007) NIX is required for programmed mitochondrial clearance during reticulocyte maturation. Proc Natl Acad Sci U S A 104(49):19500–19505

    Article  PubMed  PubMed Central  Google Scholar 

  22. Tian W, Chen J, He H, Deng Y (2013) MicroRNAs and drug resistance of breast cancer: basic evidence and clinical applications. Clin Transl Oncol 15(5):335–342

    Article  CAS  PubMed  Google Scholar 

  23. Twig G, Elorza A, Molina AJ, Mohamed H, Wikstrom JD, Walzer G, Stiles L, Haigh SE, Katz S, Las G, Alroy J, Wu M, Py BF, Yuan J, Deeney JT, Corkey BE, Shirihai OS (2008) Fission and selective fusion govern mitochondrial segregation and elimination by autophagy. EMBO J 27(2):433–446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Wystub K, Besser J, Bachmann A, Boettger T, Braun T (2013) miR-1/133a clusters cooperatively specify the cardiomyogenic lineage by adjustment of myocardin levels during embryonic heart development. PLoS Genet 9(9):e1003793

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Yorimitsu T, Klionsky DJ (2005) Autophagy: molecular machinery for self-eating. Cell Death Differ 12(Suppl 2):1542–1552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Zhang J, Ney PA (2009) Role of BNIP3 and NIX in cell death, autophagy, and mitophagy. Cell Death Differ 16(7):939–946

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Zhang Z, Hong Y, Xiang D, Zhu P, Wu E, Li W, Mosenson J, Wu WS (2015) MicroRNA-302/367 cluster governs hESC self-renewal by dually regulating cell cycle and apoptosis pathways. Stem Cell Rep 4(4):645–657

    Article  CAS  Google Scholar 

  28. Zhang Z, Xiang D, Heriyanto F, Gao Y, Qian Z, Wu WS (2013) Dissecting the roles of miR-302/367 cluster in cellular reprogramming using TALE-based repressor and TALEN. Stem Cell Rep 1(3):218–225

    Article  CAS  Google Scholar 

  29. Zhao N, Jin L, Fei G, Zheng Z, Zhong C (2014) Serum microRNA-133b is associated with low ceruloplasmin levels in Parkinson's disease. Parkinsonism Relat Disord 20(11):1177–1180

    Article  PubMed  Google Scholar 

  30. Zhong D, Huang G, Zhang Y, Zeng Y, Xu Z, Zhao Y, He X, He F (2013) MicroRNA-1 and microRNA-206 suppress LXRalpha-induced lipogenesis in hepatocytes. Cell Signal 25(6):1429–1437

    Article  CAS  PubMed  Google Scholar 

  31. Zou Z, Wu L, Ding H, Wang Y, Zhang Y, Chen X, Chen X, Zhang CY, Zhang Q, Zen K (2012) MicroRNA-30a sensitizes tumor cells to cis-platinum via suppressing beclin 1-mediated autophagy. J Biol Chem 287(6):4148–4156

    Article  CAS  PubMed  Google Scholar 

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Acknowledgement

This work was supported by NSFC (No. 31401182), by the National Basic Research Program of China (2013CB910100), by the Natural Science Foundation of Guangdong Province, China (2014A030313533), by Yangfan Plan of Talents Recruitment Grant, Guangdong, China (Yue Cai Jiao [2015] 216, 4YF14007G), by the Science and Technology Planning Project, Guangdong, China (No. 2016A020215152), by Guangdong Medical Research Foundation (A2015332), and by Research Fund of Guangdong Medical University (M2014024, M2015001).

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Correspondence to Du Feng .

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Li, W., Chen, H., Li, S., Lin, G., Feng, D. (2017). Exploring MicroRNAs on NIX-Dependent Mitophagy. In: Hattori, N., Saiki, S. (eds) Mitophagy. Methods in Molecular Biology, vol 1759. Humana Press, New York, NY. https://doi.org/10.1007/7651_2017_15

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  • DOI: https://doi.org/10.1007/7651_2017_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7749-9

  • Online ISBN: 978-1-4939-7750-5

  • eBook Packages: Springer Protocols

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