Modulated microRNA expression during adult lifespan in Caenorhabditis elegans

Aging Cell

Volumn 5, Issue 3, 2006, Pages 235-246

  Ibáñez Ventoso, Carolina ^a   Yang, Maocheng ^b   Guo, Suzhen ^a   Robins, Harlan ^c   Padgett, Richard W ^b   Driscoll, Monica ^a  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

^c INSTITUTE FOR ADVANCED STUDY   (United States)

Author keywords

Aging; Longevity; Microarray; Translational control

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; LET 7 PROTEIN; LIN 4 PROTEIN; MESSENGER RNA; MICRORNA; OLIGORIBONUCLEOTIDE; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

AGING; ARTICLE; BIOINFORMATICS; CAENORHABDITIS ELEGANS; CARCINOGENESIS; CELL FATE; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC CONSERVATION; LIFESPAN; LONGEVITY; NONHUMAN; PRIORITY JOURNAL; RNA TRANSCRIPTION; RNA TRANSLATION; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE; TRANSLATION REGULATION;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; GENE EXPRESSION REGULATION; HEALTH; INSULIN; LONGEVITY; MICRORNAS; MUSCLE, SKELETAL; REPRESSOR PROTEINS; RNA, MESSENGER; TIME FACTORS;

ANIMALIA; CAENORHABDITIS ELEGANS; NEMATODA;

EID: 33744485559     PISSN: 14749718     EISSN: 14749726     Source Type: Journal    
DOI: 10.1111/j.1474-9726.2006.00210.x     Document Type: Article

References (71)

1. Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D (2003) MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807-818.
2. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122, 553-563.
3. Bartel DP (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
4. Bartel DP, Chen CZ (2004) Micromanagers of gene expression: The potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5, 396-400.
5. Boehm M, Slack FJ (2005) A developmental timing microRNA and its target regulate life span in C. elegans. Science 310, 1954-1957.
6. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biology 3, e85.
7. Brenner S (1974) The genetics of Caenorhabditis elegans. Genetics 77, 71-94.
8. Dillin A, Crawford DK, Kenyon C (2002a) Timing requirements for insulin/ IGF-1 signaling in C. elegans. Science 298, 830-834.
9. Dillin A, Hsu AL, Arantes-Oliveira N, Lehrer-Graiwer J, Hsin H, Fraser AG, Kamath RS, Ahringer J, Kenyon C (2002b) Rates of behavior and aging specified by mitochondrial function during development. Science 298, 2398-2401.
10. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS (2003) MicroRNA targets in Drosophila. Genome Biol. 5, R1.
11. Fabian TJ, Johnson TE (1994) Production of age-synchronous mass-cultures of Caenorhabditis elegans. J. Gerontol. 49, B145-B156.
12. Fisher AL (2004) Of worms and women: Sarcopenia and its role in disability and mortality. J. Am. Geriatr. Soc. 52, 1185-1190.
13. Fraser HB, Khaitovich P, Plotkin JB, Paabo S, Eisen MB (2005) Aging and gene expression in the primate brain. PLoS Biol. 3, 1653-1661.
14. Garigan D, Hsu AL, Fraser AG, Kamath RS, Ahringer J, Kenyon C (2002) Genetic analysis of tissue aging in Caenorhabditis elegans: A role for heat-shock factor and bacterial proliferation. Genetics 161, 1101-1112.
15. Gerstbrein B, Stamatas G, Kollias N, Driscoll M (2005) In vivo spectrofluorimetry reveals endogenous biomarkers that report healthspan and dietary restriction in Caenorhabditis elegans. Aging Cell 4, 127-137.
16. Goff LA, Yang M, Bowers J, Getts RC, Padgett RW, Hart RP (2005) Rational probe optimization and enhanced detection strategy for microRNAs using microarray. RNA Biol. 2, e9-e16.
17. Golden TR, Melov S (2004) Microarray analysis of gene expression with age in individual nematodes. Aging Cell 3, 111-124.
18. Griffiths-Jones S (2004) The microRNA Registry. Nucleic Acids Res. 32, D109-D111.
19. Grosshans H, Johnson T, Reinert KL, Gerstein M, Slack FJ (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.
20. Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N (2005) MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol. 1, e13.
21. Hamilton B, Doug YQ, Shindo M, Liu WY, Odell I, Ruvkun G, Lee SS (2005) A systematic RNAi screen for longevity genes in C. elegans. Genes Dev. 19, 1544-1555.
22. Hansen M, Hsu A, Dillin A, Kenyon C (2005) New genes tied to endocrine, metabolic, and dietary regulation of lifespan from a Caenorhabditis elegans genomic RNAi screen. PLoS Genetics 1, e17.
23. Hara K, Maruki Y, Long X, Yoshino K, Oshiro N, Hidayat S, Tokunaga C, Avruch J, Yonezawa K (2002) Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell 110, 177-189.
24. He L, Hannon GJ (2004) MicroRNAs: Small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5, 522-531.
25. Herndon LA, Schmeissner PJ, Dudaronek JM, Brown PA, Listner KM, Sakano Y, Paupard MC, Hall DH, Driscoll M (2002) Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans. Nature 419, 808-814.
26. Hobert O (2004) Common logic of transcription factor and microRNA action. Trends Biochem. Sci. 29, 462-468.
27. Hsin H, Kenyon C (1999) Signals from the reproductive system regulate the lifespan of C. elegans. Nature 399, 362-366.
28. Hutvagner G, Simard MJ, Mello CC, Zamore PD (2004) Sequence-specific inhibition of small RNA function. PLoS Biol. 2, 465-475.
29. Jia K, Chen D, Riddle DL (2004) The TOR pathway interacts with the insulin signaling pathway to regulate C. elegans larval development, metabolism and life span. Development 131, 3897-3906.
30. Jing Q, Huang S, Guth S, Zarubin T, Motoyama A, Chen JM, Di Padova F, Lin SC, Gram H, Han JH (2005) Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120, 623-634.
31. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS (2004) Human microRNA targets. PLoS Biol. 2, 1862-1879.
32. Johnson TE, McCaffrey G (1985) Programmed aging or error catastrophe? An examination by two-dimensional polyacrylamide gel electrophoresis. Mech. Ageing Dev 30, 285-297.
33. Karakelides H, Sreekumaran Nair K (2005) Sarcopenia of aging and its metabolic impact. Curr. Top. Dev. Biol. 68, 123-148.
34. Kenyon C, Chang J, Gensch E, Rudner A, Tabtiang R (1993) A C. elegans mutant that lives twice as long as wild type. Nature 366, 461-464.
35. Kim SN, Rhee J-H, Song Y-H, Park DY, Hwang M, Lee S-I, Kim JE, Gim BS, Yoon JH, Kim Y-J, Kim-Ha J (2005) Age-dependent changes of gene expression in the Drosophila head. Neurobiol. Aging 26, 1083-1091.
36. Kim DH, Sarbassov DD, Ali SM, King JE, Latek RR, Erdjument-Bromage H, Tempst P, Sabatini DM (2002) mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell 110, 163-175.
37. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N (2005) Combinatorial microRNA target predictions. Nat. Genet. 37, 495-500.
38. Kwon C, Han Z, Olson EN, Srivastava D (2005) MicroRNA1 influences cardiac differentiation in Drosophila and regulates Notch signaling. Proc. Natl Acad. Sci. USA 102, 18986-18991.
39. Lai EC, Tomancak P, Williams RW, Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biol. 4, R42.
40. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862-864.
41. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
42. Lee SS, Lee RYN, Fraser AG, Kamath RS, Ahringer J, Ruvkun G (2003) A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat. Genet. 33, 40-48.
43. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115, 787-798.
44. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20.
45. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP (2003) The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991-1008.
46. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773.
47. Lund J, Tedesco P, Duke K, Wang J, Kim SK, Johnson TE (2002) Transcriptional profile of aging in C. elegans. Curr. Biol. 12, 1566-1573.
48. Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J, Chaudhuri A, Farzan-Kashani R, Zuker M, Pasquinelli AE, Ruvkun G, Sharp PA, Tabin CJ, McManus MT (2004) MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat. Genet. 36, 1079-1083.
49. Martin GM, Austad SN, Johnson TE (1996) Genetic analysis of ageing: Role of oxidative damage and environmental stresses. Nat. Genet. 13, 25-34.
50. Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, Ahringer J, Li H, Kenyon C (2003) Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature 424, 277-284.
51. Partridge L, Gems D (2002) Mechanisms of ageing: Public or private? Nat. Rev. Genet. 3, 165-175.
52. Pasquinelli AE, Ruvkun G (2002) Control of developmental timing by microRNAs and their targets. Annu. Rev. Cell Dev. Biol. 18, 495-513.
53. Pierce SB, Costa M, Wisotzkey R, Devadhar S, Homburger SA, Buchman AR, Ferguson KC, Heller J, Platt DM, Pasquinelli AA, Liu LX, Doberstein SK, Ruvkun G (2001) Regulation of DAF-2 receptor signaling by human insulin and ins-1, a member of the unusually large and diverse C. elegans insulin gene family. Genes Dev. 15, 672-686.
54. Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma XS, MacDonald PE, Pfeffer B, Tuschl T, Rajewsky N, Rorsman P, Stoffel M (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226-230.
55. Rea SL, Wu DQ, Cypser JR, Vaupel JW, Johnson TE (2005) A stress-sensitive reporter predicts longevity in isogenic populations of Caenorhabditis elegans. Nat. Genet. 37, 894-898.
56. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901-906.
57. Robins H, Li Y, Padgett RW (2005) Incorporating structure to predict microRNA targets. Proc. Natl Acad. Sci. USA 102, 4006-4009.
58. Robins H, Press WH (2005) Human microRNAs taget a funcionally distinct population of genes with AT-rich 3′ UTRs. Proc. Natl Acad. Sci. USA 102, 15557-15562.
59. Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418, 975-979.
60. Singson A, Mercer KB, L'Hernault SW (1998) The C. elegans spe-9 gene encodes a sperm transmembrane protein that contains EGF-like repeats and is required for fertilization. Cell 93, 71-79.
61. Sokol NS, Ambros V (2005) Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes Dev. 19, 2343-2354.
62. Stark A, Brennecke J, Russell RB, Cohen SM (2003) Identification of Drosophila microRNA targets. PLoS Biology 1, e60.
63. Tatar M, Bartke A, Antebi A (2003) The endocrine regulation of aging by insulin-like signals. Science 299, 1346-1351.
64. Tissenbaum HA, Guarente L (2002) Model organisms as a guide to mammalian aging. Dev. Cell 2, 9-19.
65. Watanabe Y, Yachie N, Numata K, Saito R, Kanai A, Tomita M (2006) Computational analysis of microRNA targets in Caenorhabditis elegans. Gene 365, 2-10.
66. Weindruch R, Kayo T, Lee CK, Prolla TA (2002) Gene expression profiling of aging using DNA microarrays. Mech. Ageing Dev. 123, 177-193.
67. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RHA (2005) MicroRNA expression in zebrafish embryonic development. Science 309, 310-311.
68. Wightman B, Ha I, 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.
69. Yang MC, Li Y, Padgett RW (2005) MicroRNAs: Small regulators with a big impact. Cytokine Growth Factor Rev. 16, 387-393.
70. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594-596.
71. Zhao Y, Samal E, Srivastava D (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436, 214-220.