Effect of life history on microRNA expression during C. elegans development

RNA

Volumn 17, Issue 4, 2011, Pages 639-651

  Karp, Xantha ^a,b   Hammell, Molly ^a,c   Ow, Maria C ^a   Ambros, Victor ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b NewYork Presbyterian Hospital   (United States)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

Dauer; Development; MicroRNA

Indexed keywords

MICRORNA;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BIOGENESIS; CAENORHABDITIS ELEGANS; CELL DIVISION; CELL FATE; CONTROLLED STUDY; DIAPAUSE; EMBRYO; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION PROFILING; LARVAL DEVELOPMENT; LARVAL STAGE; LIFE HISTORY; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; REAL TIME POLYMERASE CHAIN REACTION;

ANIMALS; CAENORHABDITIS ELEGANS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MICRORNAS; TRANSCRIPTION, GENETIC; UP-REGULATION;

ANIMALIA; CAENORHABDITIS ELEGANS;

EID: 79952995309     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2310111     Document Type: Article

References (65)

1. Abbott AL, Alvarez-Saavedra E, Miska EA, Lau NC, Bartel DP, Horvitz HR, Ambros V. 2005. The let-7 microRNA family members mir- 48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9: 403-414.
2. Alvarez-Saavedra E, Horvitz HR. 2010. Many families of C. elegans microRNAs are not essential for development or viability. Curr Biol 20: 367-373.
3. Antebi A, Yeh WH, Tait D, Hedgecock EM, Riddle DL. 2000. daf-12 encodes a nuclear receptor that regulates the dauer diapause and developmental age in C. elegans. Genes Dev 14: 1512-1527. (Pubitemid 30421843)
4. AppliedBiosystems. 2008. Guide to performing relative quantitation of gene expression using real-time quantitative PCR. http://www3. appliedbiosystems.com/cms/groups/mcb-support/documents/generaldocuments/ cms-042380.pdf.
5. Barriere A, Felix MA. 2005. High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations. Curr Biol 15: 1176-1184. (Pubitemid 40950514)
6. Bartel DP. 2004. MicroRNAs genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
7. Bartel DP. 2009. MicroRNAs: Target recognition and regulatory functions. Cell 136: 215-233.
8. Baugh LR, Demodena J, Sternberg PW. 2009. RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science 324: 92-94.
9. Bethke A, Fielenbach N, Wang Z, Mangelsdorf DJ, Antebi A. 2009. Nuclear hormone receptor regulation of microRNAs controls developmental progression. Science 324: 95-98.
10. Braendle C, Félix MA. 2008. Plasticity and errors of a robust developmental system in different environments. Dev Cell 15: 714-724.
11. Brenner JL, Jasiewicz KL, Fahley AF, Kemp BJ, Abbott AL. 2010. Loss of individual microRNAs causes mutant phenotypes in sensitized genetic backgrounds in C. elegans. Curr Biol 20: 1321-1325.
12. Butcher RA, Fujita M, Schroeder FC, Clardy J. 2007. Small-molecule pheromones that control dauer development in Caenorhabditis elegans. Nat Chem Biol 3: 420-422. (Pubitemid 46956322)
13. Cassada RC, Russell RL. 1975. The dauerlarva, a post-embryonic developmental variant of the nematode Caenorhabditis elegans. Dev Biol 46: 326-342.
14. Dalley BK, Golomb M. 1992. Gene expression in the Caenorhabditis elegans dauer larva: developmental regulation of Hsp90 and other genes. Dev Biol 151: 80-90.
15. de Hoon MJ, Imoto S, Nolan J, Miyano S. 2004. Open source clustering software. Bioinformatics 20: 1453-1454. (Pubitemid 38931415)
16. de Lencastre A, Pincus Z, Zhou K, Kato M, Lee SS, Slack FJ. 2010. MicroRNAs both promote and antagonize longevity in C. elegans. Curr Biol 20: 2159-2168.
17. Esquela-Kerscher A, Johnson SM, Bai L, Saito K, Partridge J, Reinert KL, Slack FJ. 2005. Post-embryonic expression of C. elegans microRNAs belonging to the lin-4 and let-7 families in the hypodermis and the reproductive system. Dev Dyn 234: 868-877. (Pubitemid 41741159)
18. Euling S, Ambros V. 1996. Reversal of cell fate determination in Caenorhabditis elegans vulval development. Development 122: 2507-2515.
19. Feinbaum R, 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.
20. Ferguson EL, Horvitz HR. 1985. Identification and characterization of 22 genes that affect the vulval cell lineages of the nematode Caenorhabditis elegans. Genetics 110: 17-72.
21. Fielenbach N, Antebi A. 2008. C. elegans dauer formation and the molecular basis of plasticity. Genes Dev 22: 2149-2165.
22. Gerisch B, 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. (Pubitemid 38559844)
23. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C. 2010. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16: 991-1006.
24. Golden TR, Melov S. 2007. Gene expression changes associated with aging in C. elegans. WormBook 2007: 1-12.
25. Golden JW, Riddle DL. 1982. A pheromone influences larval development in the nematode Caenorhabditis elegans. Science 218: 578-580.
26. Golden JW, Riddle DL. 1984. The Caenorhabditis elegans dauer larva: developmental effects of pheromone, food, and temperature. Dev Biol 102: 368-378.
27. Hall SE, Beverly M, Russ C, Nusbaum C, Sengupta P. 2010. A cellular memory of developmental history generates phenotypic diversity in C. elegans. Curr Biol 20: 149-155.
28. Hammell CM. 2008. The microRNA-argonaute complex: A platform for mRNA modulation. RNA Biol 5: 123-127.
29. Hammell M, Long D, Zhang L, Lee A, Carmack CS, Han M, Ding Y, Ambros V. 2008. mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Methods 5: 813-819.
30. Hammell CM, Karp X, Ambros V. 2009. A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans. Proc Natl Acad Sci 106: 18668-18673.
31. Harvey SC, Barker GL, Shorto A, Viney ME. 2009. Natural variation in gene expression in the early development of dauer larvae of Caenorhabditis elegans. BMC Genomics 10: 325. doi: 10.1186/1471-2164-10-325.
32. Hilgers V, Bushati N, Cohen SM. 2010. Drosophila microRNAs 263a/b confer robustness during development by protecting nascent sense organs from apoptosis. PLoS Biol 8: e1000396. doi: 10.1371/journal.pbio.1000396.
33. Holt SJ, Riddle DL. 2003. SAGE surveys C. elegans carbohydrate metabolism: evidence for an anaerobic shift in the long-lived dauer larva. Mech Ageing Dev 124: 779-800. (Pubitemid 37271953)
34. Holtz J, Pasquinelli AE. 2009. Uncoupling of lin-14 mRNA and protein repression by nutrient deprivation in Caenorhabditis elegans. RNA 15: 400-405.
35. Hu PJ. 2007. Dauer. WormBook 2007: 1-19.
36. Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
37. Ibáñez-Ventoso C, Yang M, Guo S, Robins H, Padgett RW, Driscoll M. 2006. Modulated microRNA expression during adult lifespan in Caenorhabditis elegans. Aging Cell 5: 235-246. (Pubitemid 43805613)
38. Ibáñez-Ventoso C, Vora M, Driscoll M. 2008. Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology. PLoS ONE 3: e2818. doi: 10.1371/journal.pone.0002818.
39. Jeong PY, Kwon MS, Joo HJ, Paik YK. 2009a. Molecular time-course and the metabolic basis of entry into dauer in Caenorhabditis elegans. PLoS ONE 4: e4162. doi: 10.1371/journal.pone.0004162.
40. Jeong PY, Na K, Jeong MJ, Chitwood D, Shim YH, Paik YK. 2009b. Proteomic analysis of Caenorhabditis elegans. Methods Mol Biol 519: 145-169.
41. Johnson TE, Mitchell DH, Kline S, Kemal R, Foy J. 1984. Arresting development arrests aging in the nematode Caenorhabditis elegans. Mech Ageing Dev 28: 23-40. (Pubitemid 15222463)
42. Jones SJ, Riddle DL, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, Stricklin SL, Baillie DL, Waterston R, Marra MA. 2001. Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res 11: 1346-1352.
43. Kato M, Slack FJ. 2008. microRNAs: small molecules with big roles - C. elegans to human cancer. Biol Cell 100: 71-81. (Pubitemid 351266765)
44. Kato M, de Lencastre A, Pincus Z, Slack FJ. 2009a. Dynamic expression of small non-coding RNAs, including novel micro- RNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development. Genome Biol 10: R54. doi: 10.1186/gb-2009-10-5-r54.
45. Kato M, Paranjape T, Müller RU, Ullrich R, Nallur S, Gillespie E, Keane K, Esquela-Kerscher A, Weidhaas JB, Slack FJ. 2009b. The mir-34 microRNA is required for the DNA damage response in vivo in C. elegans and in vitro in human breast cancer cells. Oncogene 28: 2419-2424.
46. Li X, Cassidy JJ, Reinke CA, Fischboeck S, Carthew RW. 2009. A microRNA imparts robustness against environmental fluctuation during development. Cell 137: 273-282.
47. 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. (Pubitemid 36459452)
48. Liu Z, Ambros V. 1991. Alternative temporal control systems for hypodermal cell differentiation in Caenorhabditis elegans. Nature 350: 162-165.
49. Liu T, Zimmerman KK, Patterson GI. 2004. Regulation of signaling genes by TGFb during entry into dauer diapause in C. elegans. BMC Dev Biol 4: 11. doi: 10.1186/1471-213X-4-11.
50. Martinez NJ, Ow MC, Barrasa MI, Hammell M, Sequerra R, Doucette-Stamm L, Roth FP, Ambros VR, Walhout AJ. 2008a. A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev 22: 2535-2549.
51. Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, Walhout AJ. 2008b. Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res 18: 2005-2015.
52. Miska EA, Alvarez-Saavedra E, Abbott AL, Lau NC, Hellman AB, McGonagle SM, Bartel DP, Ambros VR, Horvitz HR. 2007. Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 3: e215. doi: 10.1371/journal.pgen.0030215.
53. Patterson GI, Koweek A, Wong A, Liu Y, Ruvkun G. 1997. The DAF-3 Smad protein antagonizes TGF-b-related receptor signaling in the Caenorhabditis elegans dauer pathway. Genes Dev 11: 2679-2690. (Pubitemid 27452391)
54. Pradervand S, Weber J, Thomas J, Bueno M, Wirapati P, Lefort K, Dotto GP, Harshman K. 2009. Impact of normalization on miRNA microarray expression profiling. RNA 15: 493-501.
55. Rasmussen KD, Simmini S, Abreu-Goodger C, Bartonicek N, Di Giacomo M, Bilbao-Cortes D, Horos R, Von Lindern M, Enright AJ, O'Carroll D. 2010. The miR-144/451 locus is required for erythroid homeostasis. J Exp Med 207: 1351-1358.
56. Riddle DL, Albert PS. 1997. Genetic and environmental regulation of dauer larva development. In C. elegans II (ed. DL Riddle et al.), pp. 739-768. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
57. Rukov JL, Irimia M, Mork S, Lund VK, Vinther J, Arctander P. 2007. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae. Mol Biol Evol 24: 909-917. (Pubitemid 46536715)
58. Ruzanov P, Riddle DL. 2010. Deep SAGE analysis of the Caenorhabditis elegans transcriptome. Nucleic Acids Res 38: 3252-3262.
59. Ruzanov P, Riddle DL, Marra MA, McKay SJ, Jones SM. 2007. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Exp Gerontol 42: 825-839.
60. Sulston JE, Horvitz HR. 1977. Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev Biol 56: 110-156. (Pubitemid 8049332)
61. Thomas JH, Birnby DA, Vowels JJ. 1993. Evidence for parallel processing of sensory information controlling dauer formation in Caenorhabditis elegans. Genetics 134: 1105-1117. (Pubitemid 23220033)
62. Vowels JJ, Thomas JH. 1994. Multiple chemosensory defects in daf-11 and daf-21 mutants of Caenorhabditis elegans. Genetics 138: 303-316. (Pubitemid 24299276)
63. Wang J, Kim SK. 2003. Global analysis of dauer gene expression in Caenorhabditis elegans. Development 130: 1621-1634. (Pubitemid 36527521)
64. Willenbrock H, Salomon J, Søkilde R, Barken KB, Hansen TN, Nielsen FC, Møller S, Litman T. 2009. Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing. RNA 15: 2028-2034.
65. Zahler AM. 2005. Alternative splicing in C. elegans. WormBook 2005:1-13.