Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3′UTR

Nucleic Acids Research

Volumn 38, Issue 1, 2009, Pages 239-252

  Sun, Guihua ^a   Li, Haitang ^a   Rossi, John J ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN; MICRORNA; MICRORNA 223; RHOB GUANINE NUCLEOTIDE BINDING PROTEIN; TRISTETRAPROLIN; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; GENE EXPRESSION; GENE REPRESSION; GENE TARGETING; IMMUNOBLOTTING; MUTAGENESIS; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN PROCESSING; PROTEIN RNA BINDING; PROTEIN TARGETING; RNA ANALYSIS; RNA SEQUENCE; RNA TRANSLATION; SEQUENCE ANALYSIS;

3' UNTRANSLATED REGIONS; ADENINE; BASE SEQUENCE; BINDING SITES; CELL LINE; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; PROTEIN BIOSYNTHESIS; RHOB GTP-BINDING PROTEIN; RNA-BINDING PROTEINS; TRISTETRAPROLIN; URACIL;

EID: 75649129058     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp870     Document Type: Article

References (66)

1. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
2. Jackson, R.J. and Standart, N. (2007) How do microRNAs regulate gene expression? Sci. STKE, 2007, re1.
3. Lee, Y., Jeon, K., Lee, J.T., Kim, S. and Kim, V.N. (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J., 21, 4663-4670.
4. Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Radmark, O., Kim, S. et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415-419.
5. Cai, X., Hagedorn, C.H. and Cullen, B.R. (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA, 10, 1957-1966.
6. Han, J., Lee, Y., Yeom, K.H., Kim, Y.K., Jin, H. and Kim, V.N. (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev., 18, 3016-3027.
7. Okamura, K., Hagen, J.W., Duan, H., Tyler, D.M. and Lai, E.C. (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell, 130, 89-100.
8. Ruby, J.G., Jan, C.H. and Bartel, D.P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature, 448, 83-86.
9. Berezikov, E., Chung, W.J., Willis, J., Cuppen, E. and Lai, E.C. (2007) Mammalian mirtron genes. Mol. Cell, 28, 328-336.
10. Yi, R., Qin, Y., Macara, I.G. and Cullen, B.R. (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev., 17, 3011-3016.
11. Chendrimada, T.P., Gregory, R.I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K. and Shiekhattar, R. (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature, 436, 740-744.
12. Haase, A.D., Jaskiewicz, L., Zhang, H., Laine, S., Sack, R., Gatignol, A. and Filipowicz, W. (2005) TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep., 6, 961-967.
13. Filipowicz, W., Bhattacharyya, S.N. and Sonenberg, N. (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet., 9, 102-114.
14. Liu, J., Valencia-Sanchez, M.A., Hannon, G.J. and Parker, R. (2005) MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell Biol., 7, 719-723.
15. Rehwinkel, J., Behm-Ansmant, I., Gatfield, D. and Izaurralde, E. (2005) A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA, 11, 1640-1647.
16. Lewis, B.P., Burge, C.B. and Bartel, D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
17. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
18. Friedman, R.C., Farh, K.K., Burge, C.B. and Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
19. Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-158.
20. Xie, X., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S. and Kellis, M. (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature, 434, 338-345.
21. Grimson, A., Farh, K.K., Johnston, W.K., Garrett-Engele, P., Lim, L.P. and Bartel, D.P. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell, 27, 91-105.
22. Johnson, S.M., Grosshans, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K.L., Brown, D. and Slack, F.J. (2005) RAS is regulated by the let-7 microRNA family. Cell, 120, 635-647.
23. Xiao, C., Calado, D.P., Galler, G., Thai, T.H., Patterson, H.C., Wang, J., Rajewsky, N., Bender, T.P. and Rajewsky, K. (2007) MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell, 131, 146-159.
24. Kedde, M., Strasser, M.J., Boldajipour, B., Vrielink, J.A., Slanchev, K., le Sage, C., Nagel, R., Voorhoeve, P.M., van Duijse, J., Orom, U.A. et al. (2007) RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell, 131, 1273-1286.
25. Bhattacharyya, S.N., Habermacher, R., Martine, U., Closs, E.I. and Filipowicz, W. (2006) Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell, 125, 1111-1124.
26. Fabian, M.R., Mathonnet, G., Sundermeier, T., Mathys, H., Zipprich, J.T., Svitkin, Y.V., Rivas, F., Jinek, M., Wohlschlegel, J., Doudna, J.A. et al. (2009) Mammalian miRNA RISC Recruits CAF1 and PABP to Affect PABP-Dependent Deadenylation. Mol. Cell, 35, 868-880.
27. Vasudevan, S., Tong, Y. and Steitz, J.A. (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science, 318, 1931-1934.
28. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. and Segal, E. (2007) The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278-1284.
29. Long, D., Lee, R., Williams, P., Chan, C.Y., Ambros, V. and Ding, Y. (2007) Potent effect of target structure on microRNA function. Nat. Struct. Mol. Biol., 14, 287-294.
30. Didiano, D. and Hobert, O. (2008) Molecular architecture of a miRNA-regulated 3' UTR. RNA, 14, 1297-1317.
31. Didiano, D. and Hobert, O. (2006) Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat. Struct. Mol. Biol., 13, 849-851.
32. Turi, A., Loglisci, C., Salvemini, E., Grillo, G., Malerba, D. and D'Elia, D. (2009) Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining. BMC Bioinformatics, 10(Suppl. 6), S25.
33. Yoon, K., Ko, D., Doderer, M., Livi, C.B. and Penalva, L.O. (2008) Over-represented sequences located on 3' UTRs are potentially involved in regulatory functions. RNA Biol., 5, 255-262.
34. Robins, H. and Press, W.H. (2005) Human microRNAs target a functionally distinct population of genes with AT-rich 3' UTRs. Proc. Natl Acad. Sci. USA, 102, 15557-15562.
35. Sun, G., Yan, J., Noltner, K., Feng, J., Li, H., Sarkis, D.A., Sommer, S.S. and Rossi, J.J. (2009) SNPs in human miRNA genes affect biogenesis and function. RNA, 15, 1640-1651.
36. Sun, G. and Rossi, J.J. (2009) Problems associated with reporter assays in RNAi studies. RNA Biol, 6, 1-6.
37. Sun, G., Li, H. and Rossi, J.J. (2007) Cloning and detecting signature microRNAs from mammalian cells. Methods Enzymol., 427, 123-138.
38. John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C. and Marks, D.S. (2004) Human MicroRNA targets. PLoS Biol., 2, e363.
39. Fazi, F., Rosa, A., Fatica, A., Gelmetti, V., De Marchis, M.L., Nervi, C. and Bozzoni, I. (2005) A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell, 123, 819-831.
40. Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P. and Burge, C.B. (2003) Prediction of mammalian microRNA targets. Cell, 115, 787-798.
41. Hon, L.S. and Zhang, Z. (2007) The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biol., 8, R166.
42. Parker, R. and Sheth, U. (2007) P bodies and the control of mRNA translation and degradation. Mol. Cell, 25, 635-646.
43. Barreau, C., Paillard, L. and Osborne, H.B. (2005) AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res., 33, 7138-7150.
44. Richter, J.D. (2007) CPEB: a life in translation. Trends Biochem. Sci., 32, 279-285.
45. Lee, R.C., Feinbaum, R.L. and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
46. Wightman, B., Ha, I. and Ruvkun, G. (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell, 75, 855-862.
47. Doi, N., Zenno, S., Ueda, R., Ohki-Hamazaki, H., Ui-Tei, K. and Saigo, K. (2003) Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors. Curr. Biol., 13, 41-46.
48. Humphreys, D.T., Westman, B.J., Martin, D.I. and Preiss, T. (2005) MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc. Natl Acad. Sci. USA, 102, 16961-16966.
49. Pillai, R.S., Bhattacharyya, S.N., Artus, C.G., Zoller, T., Cougot, N., Basyuk, E., Bertrand, E. and Filipowicz, W. (2005) Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science, 309, 1573-1576.
50. Chu, C.Y. and Rana, T.M. (2006) Translation Repression in Human Cells by MicroRNA-Induced Gene Silencing Requires RCK/p54. PLoS Biol., 4, e210.
51. Liu, J., Rivas, F.V., Wohlschlegel, J., Yates, J.R. 3rd, Parker, R. and Hannon, G.J. (2005) A role for the P-body component GW182 in microRNA function. Nat. Cell Biol., 7, 1261-1266.
52. Sethupathy, P., Corda, B. and Hatzigeorgiou, A.G. (2006) TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA, 12, 192-197.
53. Lal, A., Navarro, F., Maher, C.A., Maliszewski, L.E., Yan, N., O'Day, E., Chowdhury, D., Dykxhoorn, D.M., Tsai, P., Hofmann, O. et al. (2009) miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements. Mol. Cell, 35, 610-625.
54. Jing, Q., Huang, S., Guth, S., Zarubin, T., Motoyama, A., Chen, J., Di Padova, F., Lin, S.C., Gram, H. and Han, J. (2005) Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell, 120, 623-634.
55. Fenger-Gron, M., Fillman, C., Norrild, B. and Lykke-Andersen, J. (2005) Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol. Cell, 20, 905-915.
56. Lykke-Andersen, J. and Wagner, E. (2005) Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1. Genes Dev., 19, 351-361.
57. Shen, B. and Goodman, H.M. (2004) Uridine addition after microRNA-directed cleavage. Science, 306, 997.
58. Song, M.G. and Kiledjian, M. (2007) 3' Terminal oligo U-tract-mediated stimulation of decapping. Rna, 13, 2356-2365.
59. Tharun, S., He, W., Mayes, A.E., Lennertz, P., Beggs, J.D. and Parker, R. (2000) Yeast Sm-like proteins function in mRNA decapping and decay. Nature, 404, 515-518.
60. Mellman, D.L., Gonzales, M.L., Song, C., Barlow, C.A., Wang, P., Kendziorski, C. and Anderson, R.A. (2008) A PtdIns4, 5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs. Nature, 451, 1013-1017.
61. Kwak, J.E. and Wickens, M. (2007) A family of poly(U) polymerases. RNA, 13, 860-867.
62. Rissland, O.S., Mikulasova, A. and Norbury, C.J. (2007) Efficient RNA polyuridylation by noncanonical poly(A) polymerases. Mol. Cell Biol., 27, 3612-3624.
63. Pique, M., Lopez, J.M., Foissac, S., Guigo, R. and Mendez, R. (2008) A combinatorial code for CPE-mediated translational control. Cell, 132, 434-448.
64. Barreau, C., Watrin, T., Beverley Osborne, H. and Paillard, L. (2006) Protein expression is increased by a class III AU-rich element and tethered CUG-BP1. Biochem. Biophys. Res. Commun., 347, 723-730.
65. Cora, D., Di Cunto, F., Caselle, M. and Provero, P. (2007) Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions. BMC Bioinformatics, 8, 174.
66. Yoon, K., Ko, D., Doderer, M., Livi, C.B. and Penalva, L.O.F. (2008) Over-represented sequences located on 3'UTR are potentially involved in regulatory functions. RNA Biol., 5, 1-8.