Profiling of REST-dependent micrornas reveals dynamic modes of expression

Frontiers in Neuroscience

Volumn , Issue MAY, 2012, Pages

  Gao, Zhengliang ^a   Ding, Peiguo ^a   Hsieh, Jenny ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Adult neurogenesis; Epigenetic; MicroRNAs; Neural stem cell; Repressor; Transcription

Indexed keywords

MICRORNA; MICRORNA 124; MICRORNA 129; MICRORNA 132; MICRORNA 149; MICRORNA 150; MICRORNA 153; MICRORNA 195; MICRORNA 2; MICRORNA 21; MICRORNA 210; MICRORNA 212; MICRORNA 298; MICRORNA 320; MICRORNA 324; MICRORNA 330; MICRORNA 345; MICRORNA 351; MICRORNA 378; MICRORNA 455; MICRORNA 9; NESTIN; RE1 SILENCING TRANSCRIPTION FACTOR; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR SOX2; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CELL PROLIFERATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; IN VITRO STUDY; MOUSE; NERVE CELL DIFFERENTIATION; NEURAL STEM CELL; NONHUMAN; UPREGULATION;

EID: 84862159614     PISSN: 16624548     EISSN: 1662453X     Source Type: Journal    
DOI: 10.3389/fnins.2012.00067     Document Type: Article

References (39)

1. Amir, R. E., Van den Veyver, I. B., Wan, M., Tran, C. Q., Francke, U., and Zoghbi, H. Y. (1999). Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat. Genet. 23, 185-188.
2. Ballas, N., Grunseich, C., Lu, D. D., Speh, J. C., and Mandel, G. (2005). REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell 121, 645-657.
3. Ballas, N., and Mandel, G. (2005). The many faces of REST oversee epigenetic programming of neuronal genes. Curr. Opin. Neurobiol. 15, 500-506.
4. Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
5. Berns, A. (2008). A tRNA with oncogenic capacity. Cell 133, 29-30.
6. Bruce, A. W., Donaldson, I. J., Wood, I. C., Yerbury, S. A., Sadowski, M. I., Chapman, M., Göttgens, B., and Buckley, N. J. (2004). Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. Proc. Natl. Acad. Sci. U.S.A. 101, 10458-10463.
7. Calabrese, J. M., Seila, A. C., Yeo, G. W., and Sharp, P. A. (2007). RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc. Natl. Acad. Sci. U.S.A. 104, 18097-18102.
8. Cao, X., Pfaff, S. L., and Gage, F. H. (2007). A functional study of miR-124 in the developing neural tube. Genes Dev. 21, 531-536.
9. Cao, X., Yeo, G., Muotri, A. R., Kuwabara, T., and Gage, F. H. (2006). Noncoding RNAs in the mammalian central nervous system. Annu. Rev. Neurosci. 29, 77-110.
10. Chen, Z. F., Paquette, A. J., and Anderson, D. J. (1998). NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis. Nat. Genet. 20, 136-142.
11. Cheng, L. C., Pastrana, E., Tavazoie, M., and Doetsch, F. (2009). miR-124 regulates adult neurogenesis in the sub-ventricular zone stem cell niche. Nat. Neurosci. 12, 399-408.
12. Conaco, C., Otto, S., Han, J. J., and Mandel, G. (2006). Reciprocal actions of REST and a microRNA promote neuronal identity. Proc. Natl. Acad. Sci. U.S.A. 103, 2422-2427.
13. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95, 14863-14868.
14. Flynt, A. S., and Lai, E. C. (2008). Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat. Rev. Genet. 9, 831-842.
15. Gao, F. B. (2010). Context-dependent functions of specific microRNAs in neuronal development. Neural Dev. 5, 25.
16. Gao, Z., Ure, K., Ding, P., Nashaat, M., Yuan, L., Ma, J., Hammer, R. E., and Hsieh, J. (2011). The master negative regulator REST/NRSF controls adult neurogenesis by restraining the neurogenic program in quiescent stem cells. J. Neurosci. 31, 9772-9786.
17. Haussecker, D., Huang, Y., Lau, A., Parameswaran, P., Fire, A. Z., and Kay, M. A. (2010). Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16, 673-695.
18. He, L., Thomson, J. M., Hemann, M. T., Hernando-Monge, E., Mu, D., Goodson, S., Powers, S., Cordon-Cardo, C., Lowe, S. W., Hannon, G. J., and Hammond, S. M. (2005). A microRNA polycistron as a potential human oncogene. Nature 435, 828-833.
19. Hsieh, J., and Gage, F. H. (2004). Epigenetic control of neural stem cell fate. Curr. Opin. Genet. Dev. 14, 461-469.
20. Jessberger, S., Nakashima, K., Clemenson, G. D. Jr., Mejia, E., Mathews, E., Ure, K., Ogawa, S., Sinton, C. M., Gage, F. H., and Hsieh, J. (2007). Epigenetic modulation of seizure-induced neurogenesis and cognitive decline. J. Neurosci. 27, 5967-5975.
21. Johnson, D. S., Mortazavi, A., Myers, R. M., and Wold, B. (2007). Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502.
22. Kempermann, G., Song, H., and Gage, F. (2008). Adult Neurogenesis. New York: Cold Spring Harbor Laboratory Press.
23. Li, X., Sanda, T., Look, A. T., Novina, C. D., and von Boehmer, H. (2011). Repression of tumor suppressor miR-451 is essential for NOTCH1-induced oncogenesis in T-ALL. J. Exp. Med. 208, 663-675.
24. Lossos, I. S., Czerwinski, D. K., Wechser, M. A., and Levy, R. (2003). Optimization of quantitative real-time RT-PCR parameters for the study of lymphoid malignancies. Leukemia 17, 789-795.
25. Mabb, A. M., Judson, M. C., Zylka, M. J., and Philpot, B. D. (2011). Angelman syndrome: insights into genomic imprinting and neurodevelopmental phenotypes. Trends Neurosci. 34, 293-303.
26. Marshall, L., Kenneth, N. S., and White, R. J. (2008). Elevated tRNA(iMet) synthesis can drive cell proliferation and oncogenic transformation. Cell 133, 78-89.
27. Mendell, J. T. (2008). miRiad roles for the miR-17-92 cluster in development and disease. Cell 133, 217-222.
28. Ming, G. L., and Song, H. (2005). Adult neurogenesis in the mammalian central nervous system. Annu. Rev. Neurosci. 28, 223-250.
29. Otto, S. J., McCorkle, S. R., Hover, J., Conaco, C., Han, J. J., Impey, S., Yochum, G. S., Dunn, J. J., Goodman, R. H., and Mandel, G. (2007). A new binding motif for the transcriptional repressor REST uncovers large gene networks devoted to neuronal functions. J. Neurosci. 27, 6729-6739.
30. Sahoo, T., del Gaudio, D., German, J. R., Shinawi, M., Peters, S. U., Person,R. E., Garnica, A., Cheung, S. W., and Beaudet, A. L. (2008). Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat. Genet. 40, 719-721.
31. Sanuki, R., Onishi, A., Koike, C., Muramatsu, R., Watanabe, S., Muranishi, Y., Irie, S., Uneo, S., Koyasu, T., Matsui, R., Chérasse, Y., Urade, Y., Watanabe, D., Kondo, M., Yamashita, T., and Furukawa, T. (2011). miR-124a is required for hippocampal axogenesis and retinal cone survival through Lhx2 suppression. Nat. Neurosci. 14, 1125-1134.
32. Singh, S. K., Kagalwala, M. N., Parker-Thornburg, J., Adams, H., and Majumder, S. (2008). REST maintains self-renewal and pluripotency of embryonic stem cells. Nature 453, 223-227.
33. Smith, B., Treadwell, J., Zhang, D., Ly, D., McKinnell, I., Walker, P. R., and Sikorska, M. (2010). Large-scale expression analysis reveals distinct microRNA profiles at different stages of human neurodevelopment. PLoS ONE 5, e11109. doi:10.1371/jour-nal.pone.0011109
34. Tamminga, J., Kathiria, P., Koturbash, I., and Kovalchuk, O. (2008). DNA damage-induced upregulation of miR-709 in the germ line down regulates BORIS to counteract aberrant DNA hypomethylation. Cell Cycle 7, 3731-3736.
35. Tsunoda, T., and Takagi, T. (1999). Estimating transcription factor bind-ability on DNA. Bioinformatics 15, 622-630.
36. Wu, J., and Xie, X. (2006). Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression. Genome Biol. 7, R85.
37. Yu, H. B., Johnson, R., Kunarso, G., and Stanton, L. W. (2011). Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells. Genome Res. 21, 1284-1293.
38. Zheng, D., Zhao, K., and Mehler, M. F. (2009). Profiling RE1/REST-mediated histone modifications in the human genome. Genome Biol. 10, R9.
39. Zuccato, C., Tartari, M., Crotti, A., Goffredo, D., Valenza, M., Conti, L., Cataudella, T., Leavitt, B. R., Hayden, M. R., Timmusk, T., Rigamonti, D., and Cattaneo, E. (2003). Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes. Nat. Genet. 35, 76-83.