Regulation of miRNA expression during neural cell specification

European Journal of Neuroscience

Volumn 21, Issue 6, 2005, Pages 1469-1477

  Smirnova, Lena ^a   Gräfe, Anja ^a   Seiler, Andrea ^b   Schumacher, Stefan ^a   Nitsch, Robert ^a   Wulczyn, F Gregory ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b FEDERAL INSTITUTE FOR RISK ASSESSMENT   (Germany)

Author keywords

Embryonic stem cells; lin 4; MicroRNA; Neural differentiation

Indexed keywords

MICRORNA;

ANIMAL CELL; ARTICLE; ASTROCYTE; BRAIN DEVELOPMENT; CELL SPECIFICITY; COMPLEMENTARITY DETERMINING REGION; GENE CLUSTER; GENE EXPRESSION REGULATION; GENETIC ANALYSIS; MOLECULAR CLONING; MOUSE; NERVE CELL; NERVE CELL CULTURE; NERVE CELL DIFFERENTIATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; STEM CELL; TRANSCRIPTION REGULATION;

ANIMALS; ANIMALS, NEWBORN; CELL DIFFERENTIATION; CELL LINE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MICE; MICRORNAS; NEURONS; STEM CELLS;

EID: 18444415448     PISSN: 0953816X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1460-9568.2005.03978.x     Document Type: Article

References (55)

1. Abrahante, J.E., Daul, A.L., Li, M., Volk, M.L., Tennessen, J.M., Miller, E.A. & Rougvie, A.E. (2003) The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev. Cell, 4, 625-637.
2. Ambros, V. (2004) The functions of animal microRNAs. Nature, 431, 350-355.
3. Banerjee, D. & Slack, F. (2002) Control of developmental timing by small temporal RNAs: a paradigm for RNA-mediated regulation of gene expression. Bioessays, 24, 119-129.
4. Bartel, D.P. (2004) MicroRNAs. Genomics, Biogenesis, Mechanism, and Function. Cell, 116, 281-297.
5. Baulcombe, D. (2004) RNA silencing in plants. Nature, 431, 356-363.
6. Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B. & Cohen, S.M. (2003) Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell, 113, 25-36.
7. Calin, G.A., Dumitru, C.D., Shimizu, M., Bichi, R., Zupo, S., Noch, E., Aldler, H., Rattan, S., Keating, M., Rai, K., Rassenti, L., Kipps, T., Negrini, M., Bullrich, F. & Croce, C.M. (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl Acad. Sci. USA, 99, 15524-15529.
8. Calin, G.A., Liu, C.G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C.D., Shimizu, M., Cimmino, A., Zupo, S., Dono, M., Dell'Aquila, M.L., Alder, H., Rassenti, L., Kipps, T.J., Bullrich, F., Negrini, M. & Croce, C.M. (2004a) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl Acad. Sci. USA, 101, 11755-11760.
9. Calin, G.A., Sevignani, C., Dumitru, C.D., Hyslop, T., Noch, E., Yendamuri, S., Shimizu, M., Rattan, S., Bullrich, F., Negrini, M. & Croce, C.M. (2004b) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl Acad. Sci. USA, 101, 2999-3004.
10. Chang, S., Johnston, R.J. Jr, Frokjaer-Jensen, C., Lockery, S. & Hobert, O. (2004) MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature, 430, 785-789.
11. Chen, C.Z., Li, L., Lodish, H.F. & Bartel, D.P. (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science, 303, 83-86.
12. Dostie, J., Mourelatos, Z., Yang, M., Sharma, A. & Dreyfuss, G. (2003) Numerous microRNPs in neuronal cells containing novel microRNAs. RNA, 9, 180-186.
13. Drejer, J., Larsson, O.M., Kvamme, E., Svenneby, G., Hertz, L. & Schousboe, A. (1985) Ontogenetic development of glutamate metabolizing enzymes in cultured cerebellar granule cells and in cerebellum in vivo. Neurochem. Res., 10, 49-62.
14. Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C. & Marks, D.S. (2003) MicroRNA targets in Drosophila. Genome Biol., 5, R1.
15. Euling, S. & Ambros, V. (1996) Heterochronic genes control cell cycle progress and developmental competence of C. elegans vulva precursor cells. Cell, 84, 667-676.
16. Hallam, S.J. & Jin, Y. (1998) lin-14 regulates the timing of synaptic remodelling in Caenorhabditis elegans. Nature, 395, 78-82.
17. He, L. & Hannon, G.J. (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nature Rev. Genet., 5, 522-531.
18. Hong, Y., Lee, R.C. & Ambros, V. (2000) Structure and function analysis of LIN-14, a temporal regulator of postembryonic developmental events in Caenorhabditis elegans. Mol. Cell Biol., 20, 2285-2295.
19. Hong, Y., Roy, R. & Ambros, V. (1998) Developmental regulation of a cyclin-dependent kinase inhibitor controls postembryonic cell cycle progression in Caenorhabditis elegans. Development, 125, 3585-3597.
20. Houbaviy, H.B., Murray, M.F. & Sharp, P.A. (2003) Embryonic stem cell-specific MicroRNAs. Dev. Cell, 5, 351-358.
21. Isshiki, T., Pearson, B., Holbrook, S. & Doe, C.Q. (2001) Drosophila neuroblasts sequentially express transcription factors which specify the temporal identity of their neuronal progeny. Cell, 106, 511-521.
22. John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C. & Marks, D.S. (2004) Human MicroRNA targets. PLoS. Biol., 2, e363.
23. Johnston, R.J. & Hobert, O. (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature, 426, 845-849.
24. Kawasaki, H. & Taira, K. (2003) Functional analysis of microRNAs during the retinoic acid-induced neuronal differentiation of human NT2 cells. Nucl. Acids Res. Suppl., 3, 243-244.
25. Kim, J., Krichevsky, A., Grad, Y., Hayes, G.D., Kosik, K.S., Church, G.M. & Ruvkun, G. (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl Acad. Sci. USA, 101, 360-365.
26. Kiriakidou, M., Nelson, P.T., Kouranov, A., Fitziev, P., Bouyioukos, C., Mourelatos, Z. & Hatzigeorgiou, A. (2004) A combined computational- experimental approach predicts human microRNA targets. Genes Dev., 18, 1165-1178.
27. Krichevsky, A.M., King, K.S., Donahue, C.P., Khrapko, K. & Kosik, K.S. (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA, 9, 1274-1281.
28. Kuwabara, T., Hsieh, J., Nakashima, K., Taira, K. & Gage, F.H. (2004) A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell, 116, 779-793.
29. Lagos-Quintana, M., Rauhut, R., Yalcin, A., Meyer, J., Lendeckel, W. & Tuschl, T. (2002) Identification of tissue-specific microRNAs from mouse. Curr. Biol., 12, 735-739.
30. Lai, E.C. (2002) MicroRNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nature Genet., 30, 363-364.
31. Lee, R.C. & Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862-864.
32. Lee, R.C., Feinbaum, R.L. & Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
33. Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P. & Burge, C.B. (2003) Prediction of mammalian microRNA targets. Cell, 115, 787-798.
34. Lin, S.Y., Johnson, S.M., Abraham, M., Vella, M.C., Pasquinelli, A., Gamberi, C., Gottlieb, E. & Slack, F.J. (2003) The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev. Cell, 4, 639-650.
35. Liu, C.G., Calin, G.A., Meloon, B., Gamliel, N., Sevignani, C., Ferracin, M., Dumitru, C.D., Shimizu, M., Zupo, S., Dono, M., Alder, H., Bullrich, F., Negrini, M. & Croce, C.M. (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl Acad. Sci. USA, 101, 9740-9744.
36. MacPherson, P.A. & McBurney, M.W. (1995) P19 Embryonal carcinoma cells: a source of cultured neurons amenable to genetic manipulation. Methods: a Companion Meth. Enzymol., 7, 238-252.
37. Maniatis, T. & Tasic, B. (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature, 418, 236-243.
38. Moss, E.G., Lee, R.C. & Ambros, V. (1997) The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell, 88, 637-646.
39. Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M. & Dreyfuss, G. (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev., 16, 720-728.
40. Musunuru, K. & Damell, R.B. (2001) Paraneoplastic neurologic disease antigens: RNA-binding proteins and signaling proteins in neuronal degeneration. Annu. Rev. Neurosci., 24, 239-262.
41. Pasquinelli, A.E. & Ruvkun, G. (2002) Control of developmental timing by micromas and their targets. Annu. Rev. Cell Dev. Biol., 18, 495-513.
42. Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R. & Ruvkun, G. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901-906.
43. Rougvie, A.E. (2001) Control of developmental timing in animals. Nature Rev. Genet., 2, 690-701.
44. Schwarz, D.S. & Zamore, P.D. (2002) Why do miRNAs live in the miRNP? Genes Dev., 16, 1025-1031.
45. Seiler, A., Visan, A., Buesen, R., Genschow, E. & Spielmann, H. (2004) Improvement of an in vitro stem cell assay for developmental toxicity: the use of molecular endpoints in the embryonic stem cell test. Reprod. Toxicol., 18, 231-240.
46. Sempere, L.F., Freemantle, S., Pitha-Rowe, I., Moss, E., Dmitrovsky, E. & Ambros, V. (2004) Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol., 5, R13.
47. Slack, F.J., Basson, M., Liu, Z., Ambros, V., Horvitz, H.R. & Ruvkun, G. (2000) The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell, 5, 659-669.
48. Stark, A., Brennecke, J., Russell, R.B. & Cohen, S.M. (2003) Identification of Drosophila MicroRNA Targets. Plos. Biol., 1, E60.
49. Steward, O. & Schuman, E.M. (2003) Compartmentalized synthesis and degradation of proteins in neurons. Neuron, 40, 347-359.
50. Suh, M.R., Lee, Y., Kim, J.Y., Kim, S.K., Moon, S.H., Lee, J.Y., Cha, K.Y., Chung, H.M., Yoon, H.S., Moon, S.Y., Kim, V.N. & Kim, K.S. (2004) Human embryonic stem cells express a unique set of microRNAs. Dev. Biol., 270, 488-498.
51. Tiedge, H., Bloom, F.E. & Richter, D. (1999) RNA, whither goest thou? Science, 283, 186-187.
52. Xu, P., Vernooy, S.Y., Guo, M. & Hay, B.A. (2003) The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol., 13, 790-795.
53. Yao, M., Bain, G. & Gottlieb, D.I. (1995) Neuronal differentiation of P19 embryonal carcinoma cells in defined media. J. Neurosci. Res., 41, 792-804.
54. Ying, Q.L. & Smith, A.G. (2003) Defined conditions for neural commitment and differentiation. Meth. Enzymol., 365, 327-341.
55. Ying, Q.L., Stavridis, M., Griffiths, D., Li, M. & Smith, A. (2003) Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nature Biotechnol., 21, 183-186.