MicroRNAs tell an evo-devo story

Nature Reviews Neuroscience

Volumn 10, Issue 10, 2009, Pages 754-759

  Kosik, Kenneth S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOGEN SYNTHASE KINASE 3BETA; HOMEODOMAIN PROTEIN; MESSENGER RNA; MICRORNA; RNA INDUCED SILENCING COMPLEX;

CELL CYCLE; CENTRAL NERVOUS SYSTEM; EVOLUTIONARY DEVELOPMENTAL BIOLOGY; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENE TARGETING; GENETIC CODE; GENETIC VARIABILITY; HOX GENE; INTRON; NEGATIVE FEEDBACK; NERVE CELL; NERVOUS SYSTEM DEVELOPMENT; NONHUMAN; NOTE; PARALOGY; PHYLOGENY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROCESSING; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSLATION; STOICHIOMETRY; SYNAPSE; TRANSCRIPTION INITIATION;

ANIMALS; BIOLOGICAL EVOLUTION; DEVELOPMENTAL BIOLOGY; HUMANS; MICRORNAS; MODELS, GENETIC; NERVOUS SYSTEM;

EID: 70349281389     PISSN: 1471003X     EISSN: 14710048     Source Type: Journal    
DOI: 10.1038/nrn2713     Document Type: Note

References (62)

1. Kosik, K. S. The neuronal microRNA system. Nature Rev. Neurosci. 7, 911-992 (2006).
2. Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854 (1993).
3. Reinhart, B. J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901-906 (2000).
4. Giraldez, A. J. et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312, 75-79 (2006).
5. Miller, G. On the origins of the nervous system. Science 325, 24-26 (2009).
6. Sakarya, O. et al. A post-synaptic scaffold at the origin of the animal kingdom. PLoS One 2, e506 (2007).
7. Davidson, E. H. & Erwin, D. H. Gene regulatory networks and the evolution of animal body plans. Science 3 11, 796-800 (2006).
8. Yekta, S., Shih, I. H. & Bartel, D. P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594-596 (2004).
9. Winter, J., Jung, S., Keller, S., Gregory, R. I. & Diederichs, S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nature Cell Biol. 11, 228-234 (2009).
10. Sempere, L. F., Cole, C. N., McPeek, M. A. & Peterson, K. J. The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J. Exp. Zool. B Mol. Dev. Evol. 306, 575-588 (2006).
11. Okamura, K. et al. The regulatory activity of microRNA* species has substantial influence on microRNA and 30′ UTR evolution. Nature Struct. Mol. Biol. 15, 354-363 (2008).
12. Wheeler, B. M. et al. The deep evolution of metazoan microRNAs. Evol. Dev. 11, 50-68 (2009).
13. Giraldez, A. J. et al. MicroRNAs regulate brain morphogenesis in zebrafish. Science 308, 833-838 (2005).
14. Sokol, N. S. & Ambros, V. Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes D ev. 19, 2343-2354 (2005).
15. Brennecke, J., Stark, A. & Cohen, S. M. Not miR-ly muscular: microRNAs and muscle development. Genes Dev. 19, 2261-2264 (2005).
16. Lim, L. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773 (2005).
17. 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 120, 15-20 (2005).
18. Papagiannakopoulos, T., Shapiro, A. & Kosik, K. S. MicroRNA-21 targets a network of key tumor-suppressive pathways in glioblastoma cells. Cancer Res. 68, 8164-8172 (2008).
19. Chi, S. W., Zang, J. B., Mele, A. & Darnell, R. B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460, 479-486 (2009).
20. Umulis, D. M., Serpe, M., O'Connor, M. B. & Othmer, H. G. Robust, bistable patterning of the dorsal surface of the Drosophila embryo. Proc. Natl Acad. Sci. USA 103, 11613-11618 (2006).
21. Wang, Y. C. & Ferguson, E. L. Spatial bistability of Dpp-receptor interactions during Drosophila dorsal-ventral patterning. Nature 434, 229-234 (2005).
22. Krichevsky, A. M., King, K. S., Donahue, C. P., Khrapko, K. & Kosik, K. S. A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9, 1274-1281 (2003).
23. Berezikov, E. et al. Diversity of microRNAs in human and chimpanzee brain. Nature Genet. 38, 1375-1377 (2006).
24. Hallam, S. J. & Jin, Y. lin-14 regulates the timing of synaptic remodelling in Caenorhabditis elegans. Nature 395, 78-82 (1998).
25. Lin, S. Y. et al. The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev. Cell 4, 639-650 (2003).
26. Abrahante, J. E. et al. The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev. Cell 4, 625-637 (2003).
27. Gierer, A. & Meinhardt, H. A theory of biological pattern formation. Kybernetik 12, 30-39 (1972).
28. Singh, N. P. & Mishra, R. K. A double-edged sword to force posterior dominance of Hox genes. Bioessays 30, 1058-1061 (2008).
29. Yekta, S., Tabin, C. J. & Bartel, D. P. MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nature Rev. Genet. 9, 789-796 (2008).
30. Chang, S., Johnston, R. J. Jr, Frokjaer-Jensen, C., Lockery, S. & Hobert, O. MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430, 785-789 (2004).
31. Chang, S., Johnston, R. J. Jr & Hobert, O. A transcriptional regulatory cascade that controls left/ right asymmetry in chemosensory neurons of C. elegans. Genes Dev. 17, 2123-2137 (2003).
32. Johnston, R. J. & Hobert, O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845-849 (2003).
33. Johnston, R. J. Jr, Chang, S., Etchberger, J. F., Ortiz, C. O. & Hobert, O. MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc Natl. Acad. Sci. USA 102, 12449-12454 (2005).
34. Xu, N., Papagiannakopoulos, T., Pan, G., Thomson, J. A. & Kosik, K. S. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell 137, 647-658 (2009).
35. Justman, Q. A., Serber, Z., Ferrell, J. E. Jr, El-Samad, H. & Shokat, K. M. Tuning the activation threshold of a kinase network by nested feedback loops. Science 324, 509-512 (2009).
36. Choi, P. S. et al. Members of the miRNA-200 family regulate olfactory neurogenesis. Neuron 57, 41-55 (2008).
37. Jan, Y. N. & Jan, L. Y. Neronal cell fate specification in Drosophila. Curr. Opin. Neurobiol. 4, 8-13 (1994).
38. Hobert, O. Regulatory logic of neuronal diversity: terminal selector genes and selector motifs. Proc. Natl Acad. Sci. USA 105, 20067-20071 (2008).
39. Conaco, C., Otto, S., Han, J. J. & Mandel, G. Reciprocal actions of REST and a microRNA promote neuronal identity. Proc. Natl Acad. Sci. USA 103, 2422-2427 (2006).
40. Hornstein, E. & Shomron, N. Canalization of development by microRNAs. Nature Genet. 38, S20-S24 (2006).
41. Schratt, G. M. et al. A brain-specific microRNA regulates dendritic spine development. Nature 439, 283-289 (2006).
42. Lisman, J. Actin's actions in LTP-induced synapse growth. Neuron 38, 361-362 (2003).
43. Siegel, G. et al. A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Nature Cell Biol. 11, 705-716 (2009).
44. Kang, R. et al. Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature 456, 904-909 (2008).
45. Jones, T. L., Degtyarev, M. Y. & Backlund, P. S. Jr. The stoichiometry of Gαs palmitoylation in its basal and activated states. Biochemistry 36, 7185-7191 (1997).
46. Buhl, A. M., Johnson, N. L., Dhanasekaran, N. & Johnson, G. L. Gα12 and Gα13 stimulate Rho-dependent stress fiber formation and focal adhesion assembly. J. Biol. Chem. 270, 24631-24634 (1995).
47. Vo, N. et al. A cAMP-response element binding protein-induced microRNA regulates neuronal morphogenesis. Proc. Natl Acad. Sci. USA 102, 16426-16431 (2005).
48. Nudelman, A. S. et al. Neuronal activity rapidly induces transcription of the CREB-regulated microRNA-132, in vivo. Hippocampus 25 Jun 2009 (doi:10.1002/hipo.20646).
49. Wayman, G. A. et al. An activity-regulated microRNA controls dendritic plasticity by down-regulating p250GAP. Proc. Natl Acad. Sci. USA 105, 9093-10908 (2008).
50. Cheng, H. Y. et al. microRNA modulation of circadian-clock period and entrainment. Neuron 54, 813-829 (2007).
51. Larroux, C. et al. Genesis and expansion of metazoan transcription factor gene classes. Mol. Biol. Evol. 25, 980-996 (2008).
52. Philippe, H. et al. Phylogenomics revives traditional views on deep animal relationships. Curr. Biol. 19, 706-712 (2009).
53. Berezikov, E. et al. Diversity of microRNAs in human and chimpanzee brain. Nature Genet. 38, 1375-1377 (2006).
54. Liang, H. & Li, W. H. Lowly expressed human microRNA genes evolve rapidly. Mol. Biol. Evol. 26, 1195-1198 (2009).
55. King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107-116 (1975).
56. Taft, R. J., Pheasant, M. & Mattick, J. S. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29, 288-299 (2007).
57. Heimberg, A. M., Sempere, L. F., Moy, V. N., Donoghue, P. C. & Peterson, K. J. MicroRNAs and the advent of vertebrate morphological complexity. Proc. Natl Acad. Sci USA 105, 2946-2950 (2008).
58. Kirschner, M. & Gerhart, J. Evolvability. Proc. Natl Acad. Sci. USA 95, 8420-8427 (1998).
59. Chen, K. & Rajewsky, N. The evolution of gene regulation by transcription factors and microRNAs. Nature Rev. Genet. 8, 93-103 (2007).
60. Liu, N. et al. The evolution and functional diversification of animal microRNA genes. Cell Res. 18, 985-996 (2008).
61. Bartel, D. P. & Chen, C. Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature Rev. Genet. 5, 396-400 (2004).
62. Griffiths-Jones, S., Saini, H. K., van Dongen, S. & Enright, A. J. miRBase: tools for microRNA genomics Nucleic Acids Res. 36, D154-D158 (2008).