Intrinsic and extrinsic regulators of developmental timing: From miRNAs to nutritional cues

Development

Volumn 132, Issue 17, 2005, Pages 3787-3798

  Rougvie, Ann E ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; COHESIN; CYTOPLASM PROTEIN; DROSOPHILA PROTEIN; ECDYSONE; ECDYSONE RECEPTOR; EPIDERMAL GROWTH FACTOR; INSULIN RECEPTOR; MICRORNA; MITOGEN ACTIVATED PROTEIN KINASE; RAS PROTEIN; TARGET OF RAPAMYCIN KINASE;

ACCURACY; CAENORHABDITIS ELEGANS; CELL DIFFERENTIATION; CELL LINEAGE; CIRCADIAN RHYTHM; DROSOPHILA; EPIDERMIS; FLY; GENE EXPRESSION; GENE MUTATION; INSECT DEVELOPMENT; LARVAL STAGE; METAMORPHOSIS; MICROBIAL METABOLISM; MORPHOGENESIS; NERVOUS SYSTEM DEVELOPMENT; NONHUMAN; NUTRITIONAL STATUS; PARASITE DEVELOPMENT; PRIORITY JOURNAL; PROTEIN FUNCTION; PUPATION; REPRODUCIBILITY; REVIEW; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; TEMPERATURE;

ANIMALS; CAENORHABDITIS ELEGANS; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; MICRORNAS; NUTRITION PHYSIOLOGY; TIME FACTORS;

CAENORHABDITIS ELEGANS; INSECTA; METAZOA;

EID: 26244440240     PISSN: 09501991     EISSN: None     Source Type: Journal    
DOI: 10.1242/dev.01972     Document Type: Review

References (88)

1. Abrahante, J. E., Miller, E. A. and Rougvie, A. E. (1998). Identification of heterochronic mutants in Caenorhabditis elegans: temporal misexpression of a collagen::green fluorescent protein fusion gene. Genetics 149, 1335-1351.
2. Abrahante, J. E., Daul, A. L., Li, M., Volk, M. L., Tennessen, J. M., Miller, E. A. and Rougvie, A. E. (2003). The Caenorhabditis elegans hunchback-like gene lin-57/hbl-I controls developmental time and is regulated by microRNAs. Dev. Cell 4, 625-637.
3. Ambros, V. (1989). A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans. Cell 57, 49-57.
4. Ambros, V. (2004). The functions of animal microRNAs. Nature 431, 350-355.
5. Ambros, V. and Horvitz, H. R. (1984). Heterochronic mutants of the nematode Caenorhabditis elegans. Science 226, 409-416.
6. Ambros, V. and Horvitz, H. R. (1987). The lin-14 locus of Caenorhabditis elegans controls the time of expression of specific postembryonic developmental events. Genes Dev. 1, 398-414.
7. Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. and Jewell, D. (2003). MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807-818.
8. Antebi, A., Culotti, J. G. and Hedgecock, E. M. (1998). daf-12 regulates developmental age and the dauer alternative in Caenorhabditis elegans. Development 125, 1191-1205.
9. Antebi, A., Yeh, W. H., Tait, D., Hedgecock, E. M. and Riddle, D. L. (2000). daf-12 encodes a nuclear receptor that regulates the dauer diapause and developmental age in C. elegans. Genes Dev. 14, 1512-1527.
10. Arasu, P. A., Wightman, B. and Ruvkun, G. (1991). Temporal regulation of lin-14 by the antagonistic action of two other heterochronic genes, lin-4 and lin-28. Genes Dev. 5, 1825-1833.
11. Banerjee, D., Kwok, A., Lin, S. Y. and Slack, F. J. (2005). Developmental timing in C. elegans is regulated by kin-20 and tim-1, homologs of core circadian clock genes.Dev. Cell 8, 287-295.
12. Bartel, D. P. and Chen, C. Z. (2004). Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5, 396-400.
13. Bashirullah, A., Pasquinelli, A. E., Kiger, A. A., Perrimon, N., Ruvkun, G. and Thummel, C. S. (2003). Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis. Dev. Biol. 259, 1-8.
14. Bateman, J. M. and McNeill, H. (2004). Temporal control of differentiation by the insulin receptor/tor pathway in Drosophila. Cell 119, 87-96.
15. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B. and 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.
16. Calin, G. A., Dumitru, C. D., Shimizu, M., Bichi, R., Zupo, S., Noch, E., Aldler, H., Rattan, S., Keating, M., Rai, K. et al. (2002). Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at l3q14 in chronic lymphocytic leukemia. Proc. Natl. Acad. Sci. USA 99, 15524-15529.
17. Calin, G. A., Sevignani, C., Dumitru, C. D., Hyslop, T., Noch, E., Yendamuri, S., Shimizu, M., Rattan, S., Bullrich, F., Negrini, M. et al. (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl. Acad. Sci. USA 101, 2999-3004.
18. Cassada, R. C. and Russell, R. L. (1975). The dauer larva, a post-embryonic developmental variant of the nematode Caenorhabditis elegans. Dev. Biol. 46, 326-342.
19. Chalfie, M., Horvitz, H. R. and Sulston, J. E. (1981). Mutations that lead to reiterations in the cell lineages of C. elegans. Cell 24, 59-69.
20. Chan, R. C., Chan, A., Jeon, M., Wu, T. F., Pasqualone, D., Rougvie, A. E. and Meyer, B. J. (2003). Chromosome cohesion is regulated by a clock gene paralogue TIM-1. Nature 423, 1002-1009.
21. Chang, S., Johnston, R. J., Jr, Frokjaer-Jensen, C., Lockery, S. and Hobert, O. (2004). MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430, 785-789.
22. Clayton, J. D., Kyriacou, C. P. and Reppert, S. M. (2001). Keeping time with the human genome. Nature 409, 829-831.
23. Darlington, T. K., Wager-Smith, K., Ceriani, M. F., Staknis, D., Gekakis, N., Steeves, T. D. L., Weitz, C. J., Takahashi, J. S. and Kay, S. A. (1998). Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim. Science 280, 1599-1603.
24. Doench, J. G. and Sharp, P. A. (2004). Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504-511.
25. Feinbaum, R. and Ambros, V. (1999). The timing of lin-4 RNA accumulation controls the timing of postembryonic developmental events in Caenorhabditis elegans. Dev. Biol. 210, 87-95.
26. Gerisch, B. and Antebi, A. (2004). Hormonal signals produced by DAF-9/cytochrome P450 regulate C. elegans dauer diapause in response to environmental cues. Development 131, 1765-1776.
27. Gerisch, B., Weitzel, C., Kober-Eisermann, C., Rottiers, V. and Antebi, A. (2001). A hormonal signaling pathway influencing C. elegans metabolism, reproductive development, and life span. Dev. Cell 1, 841-851.
28. Glossop, N. R. and Hardin, P. E. (2002). Central and peripheral circadian oscillator mechanisms in flies and mammals. J. Cell Sci. 115, 3369-3377.
29. Großhans, H., Johnson, T., Reinert, K. L., Gerstein, M. and Slack, F. J. (2005). The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev. Cell 8, 321-330.
30. Grosskortenhaus, R., Pearson, B. J., Marusich, A. and Doe, C. Q. (2005). Regulation of temporal identity transitions in Drosophila neuroblasts. Dev. Cell 8, 193-202.
31. Hallam, S. J. and Jin, Y. (1998). lin-14 regulates the timing of synaptic remodeling in Caenorhabditis elegans. Nature 395, 78-82.
32. Hara, K., Maruki, Y., Long, X., Yoshino, K., Oshiro, N., Hidayat, S., Tokunaga, C., Avruch, J. and Yonezawa, K. (2002). Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell 110, 177-189.
33. He, L. and Hannon, G. J. (2004). MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5, 522-531.
34. Hime, G. and Saint, R. (1992). Zygotic expression of the pebble locus is required for cytokinesis during the postblastoderm mitoses of Drosophila. Development 114, 165-171.
35. Isshiki, T., Pearson, B., Holbrook, S. and Doe, C. Q. (2001). Drosophila neuroblasts sequentially express transcription factors which specify the temporal identity of their neuronal progeny. Cell 106, 511-521.
36. Jeon, M., Gardner, H. F., Miller, E. A., Deshler, J. and Rougvie, A. E. (1999). Similarity of the C. elegans developmental timing protein LIN-42 to circadian rhythm proteins. Science 286, 1141-1146.
37. Jia, K., Albert, P. S. and Riddle, D. L. (2002). DAF-9, a cytochrome P450 regulating C. elegans larval development and adult longevity. Development 129, 221-231.
38. Jia, K., Chen, D. and Riddle, D. L. (2004). The TOR pathway interacts with the insulin signaling pathway to regulate C. elegans larval development, metabolism and life span. Development 131, 3897-3906.
39. 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.
40. Johnston, R. J. and Hobert, O. (2003). A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845-849.
41. Kanai, M. I., Okabe, M. and Hiromi, Y. (2005). seven-up Controls switching of transcription factors that specify temporal identifies of Drosophila neuroblasts. Dev. Cell 8, 203-213.
42. Kidner, C. A. and Martienssen, R. A. (2005). The developmental role of microRNA in plants. Curr. Opin. Plant Biol. 8, 38-44.
43. Kippert, F., Saunders, D. S. and Blaxter, M. L. (2002). Caenorhabditis elegans has a circadian clock. Curr. Biol. 12, R47-R49.
44. Kiriakidou, M., Nelson, P. T., Kouranov, A., Fitziev, P., Bouyioukos, C., Mourelatos, Z. and Hatzigeorgiou, A. (2004). A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 18, 1165-1178.
45. Kloosterman, W. P., Wienholds, E., Ketting, R. F. and Plasterk, R. H. (2004). Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res. 32, 6284-6291.
46. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science 294, 853-858.
47. Lagos-Quintana, M., Rauhut, R., Yalcin, A., Meyer, J., Lendeckel, W. and Tuschl, T. (2002). Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12, 735-739.
48. Lau, N. C., Lim, L. P., Weinstein, E. G. and Bartel, D. P. (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862.
49. Lee, C., Bae, K. and Edery, I. (1999). PER and TIM inhibit the DNA binding activity of a Drosophila CLOCK-CYC/dBMAL1 heterodimer without disrupting formation of the heterodimer: a basis for circadian transcription. Mol. Cell. Biol. 19, 5316-5325.
50. 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.
51. Lee, Y. S., Kim, H. K., Chung, S., Kim, K. S. and Dutta, A. (2005). Depletion of human micro-RNA miR-125b reveals that it is critical for the proliferation of differentiated cells but not for the down-regulation of putative targets during differentiation. J. Biol. Chem. 280, 16635-16641.
52. Lehmann, R. and Nusslein-Volhard, C. (1987). hunchback, a gene required for segmentation of an anterior and posterior region of the Drosophila embryo. Dev. Biol. 119, 402-417.
53. Lehner, C. F. (1992). The pebble gene is required for cytokinesis in Drosophila. J. Cell Sci. 103, 1021-1030.
54. Lim, L. P., Lau, N. C., Weinstein, E. G., Abdelhakim, A., Yekta, S., Rhoades, M. W., Burge, C. B. and Bartel, D. P. (2003). The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991-1008.
55. Lin, S. Y., Johnson, S. M., Abraham, M., Vella, M. C., Pasquinelli, A., Gamberi, C., Gottlieb, E. and 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.
56. Liu, Z. and Ambros, V. (1989). Heterochronic genes control the stage-specific initiation and expression of the dauer larva developmental program in Caenorhabditis elegans. Genes Dev. 3, 2039-2049.
57. Long, X., Spycher, C., Han, Z. S., Rose, A. M., Muller, F. and Avruch, J. (2002). TOR deficiency in C. elegans causes developmental arrest and intestinal atrophy by inhibition of mRNA translation. Curr. Biol. 12, 1448-1461.
58. Long, X., Muller, F. and Avruch, J. (2004). TOR action in mammalian cells and in Caenorhabditis elegans. Curr. Top. Microbiol. Immunol. 279, 115-138.
59. Mak, H. Y. and Ruvkun, G. (2004). Intercellular signaling of reproductive development by the C. elegans DAF-9 cytochrome P450. Development 131, 1777-1786.
60. Moss, E. G. and Tang, L. (2003). Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites. Dev. Biol. 258, 432-442.
61. Moss, E. G., Lee, R. C. and 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.
62. Nawathean, P. and Rosbash, M. (2004). The doubletime and CKII kinases collaborate to potentiate Drosophila PER transcriptional repressor activity. Mol. Cell 13, 213-223.
63. Nelson, P. T., Hatzigeorgiou, A. G. and Mourelatos, Z. (2004). miRNP:mRNA association in polyribosomes in a human neuronal cell line. RNA 10, 387-394.
64. Neufeld, T. P. (2004). Genetic analysis of TOR signaling in Drosophila. Curr. Top. Microbiol. Immunol. 279, 139-152.
65. Olsen, P. H. and Ambros, V. (1999). The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216, 671-680.
66. Pasquinelli, A. E., Reinhart, B. J., Slack, F., Martindale, M. Q., Kuroda, M. I., Maller, B., Hayward, D. C., Ball, E. E., Degnan, B., Muller, P. et al. (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86-89.
67. Pepper, A. S., McCane, J. E., Kemper, K., Yeung, D. A., Lee, R. C., Ambros, V. and Moss, E. G. (2004). The C. elegans heterochronic gene lin-46 affects developmental timing at two larval stages and encodes a relative of the scaffolding protein gephyrin. Development 131, 2049-2059.
68. Poy, M. N., Etiasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., Macdonald, P. E., Pfeffer, S., Tuschl, T., Rajewsky, N., Rorsman, P. et al. (2004). A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226-230.
69. Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., Horvitz, H. R. and Ruvkun, G. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901-906.
70. Riddiford, L. M. (1993). Hormone receptors and the regulation of insect metamorphosis. Receptor 3, 203-209.
71. Rougvie, A. E. and Ambros, V. (1995). The heterochronic gene lin-29 encodes a zinc finger protein that controls a terminal differentiation event in C. elegans. Development 121, 2491-2500.
72. Ruvkun, G. and Giusto, J. (1989). The Caenorhabditis elegans heterochronic gene lin-14 encodes a nuclear protein that forms a temporal developmental switch. Nature 338, 313-319.
73. Saigusa, T., Ishizaki, S., Watabiki, S., Ishii, N., Tanakadate, A., Tamai, Y. and Hasegawa, K. (2002). Circadian behavioural rhythm in Caenorhabditis elegans. Curr. Biol. 12, R46-R47.
74. Seggerson, K., Tang, L. and Moss, E. G. (2002). Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev. Biol. 243, 215-225.
75. Sempere, L. F., Dubrovsky, E. B., Dubrovskaya, V. A., Berger, E. M. and Ambros, V. (2002). The expression of the let-7 small regulatory RNA is controlled by ecdysone during metamorphosis in Drosophila melanogaster. Dev. Biol. 244, 170-179.
76. Sempere, L. F., Freemantle, S., Pitha-Rowe, I., Moss, E., Dmitrovsky, E. and 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.
77. Skeath, J. B. and Thor, S. (2003). Genetic control of Drosophila nerve cord development. Curr. Opin. Neurobiol. 13, 8-15.
78. Slack, F. and Ruvkun, G. (1997). Temporal pattern formation by heterochronic genes. Annu. Rev. Genet. 31, 611-634.
79. Slack, F.J., Basson, M., Liu, Z., Ambros, V., Horvitz, H. R. and 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.
80. Sonoda, J. and Wharton, R. P. (2001). Drosophila Brain Tumor is a translational repressor. Genes Dev. 15, 762-773.
81. Takamizawa, J., Konishi, H., Yanagisawa, K., Tomida, S., Osada, H., Endoh, H., Harano, T., Yatabe, Y., Nagino, M., Nimura, Y. et al. (2004). Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 64, 3753-3756.
82. Tautz, D., Lehmann, R., Schnorch, H., Schuh, R., Seifert, E., Keinlin, A., Jones, K. and Jackle, H. (1987). Finger protein of novel structure encoded by hunchback, a second member of the gap class of Drosohila segmentation genes. Nature 327, 383-389.
83. Thummel, C. S. (2001). Molecular mechanisms of developmental timing in C. elegans and Drosophila. Dev. Cell 1, 453-465.
84. Wienholds, E., Kloosterman, W. P., Miska, E., Alvarez-Saavedra, E., Berezikov, E., de Bruijn, E., Horvitz, R. H., Kauppinen, S. and Plasterk, R. H. (2005). MicroRNA expression in Zebrafish embryonic development. Science (in press).
85. Wightman, B., Burglin, T. R., Gatto, J., Arasu, P. and Ruvkun, G. (1991). Negative regulatory sequences in the lin-14 3′-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development. Genes Dev. 5, 1813-1824.
86. 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.
87. Wolff, T. (2003). EGF receptor signaling: putting a new spin on eye development. Curr. Biol. 13, R813-R814.
88. Xu, P., Vernooy, S. Y., Guo, M. and Hay, B. A. (2003). The Drosophila microRNA miR-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13, 790-795.