MiRNA-Target interaction reveals cell-specific post-transcriptional regulation in mammalian cell lines

International Journal of Molecular Sciences

Volumn 17, Issue 1, 2016, Pages

  Kulkarni, Varun ^a   Naqvi, Afsar Raza ^a   Uttamani, Juhi Raju ^a   Nares, Salvador ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

Ago 2 (Argonaute 2); Cell lines; Gene regulation; MicroRNA

Indexed keywords

MICRORNA; PLASMID VECTOR; MESSENGER RNA; MIRNLET7 MICRORNA, HUMAN; RNA INDUCED SILENCING COMPLEX;

ANIMAL CELL; ARTICLE; BINDING SITE; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; FLOW CYTOMETRY; FLUORESCENCE MICROSCOPY; GENE EXPRESSION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; LUCIFERASE ASSAY; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; REGULATORY MECHANISM; REPORTER GENE; RNA ISOLATION; RNA PROCESSING; WESTERN BLOTTING; ANIMAL; CHLOROCEBUS AETHIOPS; COS CELL LINE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HELA CELL LINE; HEP-G2 CELL LINE; MOUSE; MUTATION; NIH 3T3 CELL LINE; PROTEIN SYNTHESIS; UMBILICAL VEIN ENDOTHELIAL CELL;

ANIMALS; CELL LINE; CERCOPITHECUS AETHIOPS; COS CELLS; GENE EXPRESSION REGULATION; GENES, REPORTER; HELA CELLS; HEP G2 CELLS; HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS; HUMANS; MICE; MICRORNAS; MUTATION; NIH 3T3 CELLS; PROTEIN BIOSYNTHESIS; RNA, MESSENGER; RNA-INDUCED SILENCING COMPLEX; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 84954286596     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms17010072     Document Type: Article

References (34)

1. Lee, R.C.; Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001, 294, 862-864. [CrossRef] [PubMed]
2. miRBase. Available online: http://www.mirbase.org/ (accessed on 3 July 2014).
3. Bentwich, I.; Avniel, A.; Karov, Y.; Aharonov, R.; Gilad, S.; Barad, O.; Barzilai, A.; Einat, P.; Einav, U.; Meiri, E.; et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 2005, 37, 766-770.
4. Bartel, D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004, 116, 281-297. [CrossRef]
5. He, L.; Hannon, G.J. MicroRNAs: Small RNAs with a big role in gene regulation. Nat. Rev. Genet. 2004, 5, 522-531. [CrossRef] [PubMed]
6. Lewis, B.P.; Burge, C.B.; Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120, 15-20. [CrossRef] [PubMed]
7. Berezikov, E.; Guryev, V.; van de Belt, J.;Wienholds, E.; Plasterk, R.H.; Cuppen, E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005, 120, 21-24. [CrossRef] [PubMed]
8. Zeng, Y. Principles of micro-RNA production and maturation. Oncogene 2006, 25, 6156-6162. [CrossRef] [PubMed]
9. Kim, V.N.; Han, J.; Siomi, M.C. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 2009, 10, 126-139. [CrossRef] [PubMed]
10. Carthew, R.W.; Sontheimer, E.J. Origins and Mechanisms of miRNAs and siRNAs. Cell 2009, 136, 642-655. [CrossRef] [PubMed]
11. Lagos-Quintana, M.; Rauhut, R.; Lendeckel, W.; Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 2001, 294, 853-858. [CrossRef] [PubMed]
12. O'Connell, R.M.; Rao, D.S.; Chaudhuri, A.A.; Baltimore, D. Physiological and pathological roles for microRNAs in the immune system. Nat. Rev. Immunol. 2010, 10, 111-122. [CrossRef] [PubMed]
13. Small, E.M.; Olson, E.N. Pervasive roles of microRNAs in cardiovascular biology. Nature 2011, 469, 336-342. [CrossRef] [PubMed]
14. Lu, J.; Getz, G.; Miska, E.A.; Alvarez-Saavedra, E.; Lamb, J.; Peck, D.; Alejandro, S.C.; Ebert, B.L.; Mak, R.H.; Ferrando, A.A. MicroRNA expression profiles classify human cancers. Nature 2005, 435, 834-838. [CrossRef] [PubMed]
15. Nares, S.; Moutsopoulos, N.M.; Angelov, N.; Rangel, Z.G.; Munson, P.J.; Sinha, N.;Wahl, S.M. Rapid myeloid cell transcriptional and proteomic responses to periodontopathogenic Porphyromonas gingivalis. Am. J. Pathol. 2009, 174, 1400-1414. [CrossRef] [PubMed]
16. Naqvi, A.R.; Fordham, J.B.; Nares, S. miR-24, miR-30b, and miR-142-3p regulate phagocytosis in myeloid inflammatory cells. J. Immunol. 2015, 194, 1916-1927. [CrossRef] [PubMed]
17. Doench, J.G.; Sharp, P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 2004, 18, 504-511. [CrossRef] [PubMed]
18. Valencia-Sanchez, M.A.; Liu, J.; Hannon, G.J.; Parker, R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 2006, 20, 515-524. [CrossRef] [PubMed]
19. Pasquinelli, A.E. MicroRNAs and their targets: Recognition, regulation and an emerging reciprocal relationship. Nat. Rev. Genet. 2012, 13, 271-282. [CrossRef] [PubMed]
20. Van Rooij, E.; Purcell, A.L.; Levin, A.A. Developing microRNA therapeutics. Circ. Res. 2012, 110, 496-507. [CrossRef] [PubMed]
21. Zhang, Y.; Wang, Z.; Gemeinhart, R.A. Progress in MicroRNA Delivery. J. Control. Release 2013, 172, 962-974. [CrossRef] [PubMed]
22. Engels, B.M.; Hutvagner, G. Principles and effects of microRNA-mediated post-transcriptional gene regulation. Oncogene 2006, 25, 6163-6169. [CrossRef] [PubMed]
23. Poy, M.N.; Eliasson, L.; Krutzfeldt, J.; Kuwajima, S.; Ma, X.S.; MacDonald, P.E.; Pfeffer, S.; Tuschl, T.; Rajewsky, N.; Rorsman, P. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 2004, 432, 226-230. [CrossRef] [PubMed]
24. Brennecke, J.; Hipfner, D.R.; Stark, A.; Russell, R.B.; Cohen, S.M. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 2003, 113, 25-35. [CrossRef]
25. Cimmino, A.; Calin, G.A.; Fabbri, M.; Iorio, M.V.; Ferracin, M.; Shimizu, M.; Wojcik, S.E.; Aqeilan, R.I.; Zupo, S.; Dono, M.; et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc. Nat. Acad. Sci. USA 2005, 102, 13944-13949. [CrossRef] [PubMed]
26. Zeng, Y.; Yi, R.; Cullen, B.R. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc. Nat. Acad. Sci. USA 2003, 100, 9779-9784. [CrossRef] [PubMed]
27. Kiriakidou, M.; Nelson, P.T.; Kouranov, A.; Fitziev, P.; Bouyioukos, C.; Mourelatos, Z.; Hatzigeorgiou, A. A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 2004, 18, 1165-1178. [CrossRef] [PubMed]
28. Hendrickson, D.G.; Hogan, D.J.; McCullough, H.L.; Myers, J.W.; Herschlag, D.; Ferrell, J.E.; Brown, P.O. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol. 2009, 7, e1000238. [CrossRef] [PubMed]
29. Kedersha, N.; Chen, S.; Gilks, N.; Li, W.; Miller, I.J.; Stahl, J.; Anderson, P. Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules. Mol. Biol. Cell 2002, 13, 195-210. [CrossRef] [PubMed]
30. Kedersha, N.; Stoecklin, G.; Ayodele, M.; Yacono, P.; Lykke-Andersen, J.; Fritzler, M.J.; Scheuner, D.; Kaufman, R.J.; Golan, D.E.; Anderson, P. Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. J. Cell Biol. 2005, 20, 871-884. [CrossRef] [PubMed]
31. Gibbings, D.J.; Ciaudo, C.; Erhardt, M.; Voinnet, O. Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nat. Cell Biol. 2009, 11, 1143-1149. [CrossRef] [PubMed]
32. Tourrière, H.; Chebli, K.; Zekri, L.; Courselaud, B.; Blanchard, J.M.; Bertrand, E.; Tazi, J. The RasGAP-associated endoribonuclease G3BP assembles stress granules. J. Cell Biol. 2003, 160, 823-831. [CrossRef] [PubMed]
33. Van Dijk, E.; Cougot, N.; Meyer, S.; Babajko, S.; Wahle, E.; Séraphin, B. Human Dcp2: A catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 2002, 21, 6915-6924. [CrossRef] [PubMed]
34. Eulalio, A.; Behm-Ansmant, I.; Schweizer, D.; Izaurralde, E. P-body formation is a consequence, not the cause, of RNA-mediated gene silencing. Mol. Cell. Biol. 2007, 27, 3970-3981. [CrossRef] [PubMed]