Functional Analysis of Neuronal MicroRNAs in Caenorhabditis elegans Dauer Formation by Combinational Genetics and Neuronal miRISC Immunoprecipitation

PLoS Genetics

Volumn 9, Issue 6, 2013, Pages

  Than, Minh T ^a   Kudlow, Brian A ^a   Han, Min ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC GMP; MICRORNA; NEURONAL MIRNA INDUCED SILENCING COMPLEX; PROTEIN AIN 1; PROTEIN UNC 3; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; CAENORHABDITIS ELEGANS; COMBINATIONAL GENETICS; DAUER; GENE CONTROL; GENE INTERACTION; GENE MUTATION; GENETICS; IMMUNOPRECIPITATION; LARVAL STAGE; MICROARRAY ANALYSIS; MOLECULAR CLONING; NERVE CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DEGRADATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SIGNAL TRANSDUCTION; STRESS; TRANSCRIPTION REGULATION;

ANIMALS; CAENORHABDITIS ELEGANS; CARRIER PROTEINS; CYCLIC GMP; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MICRORNAS; NEURONS; RNA, MESSENGER; RNA-INDUCED SILENCING COMPLEX; SIGNAL TRANSDUCTION;

CAENORHABDITIS ELEGANS;

EID: 84879673279     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003592     Document Type: Article

References (42)

1. Leung AK, Sharp PA, (2011) MicroRNA functions in stress responses. Mol Cell 40: 205-215.
2. Alvarez-Saavedra E, Horvitz HR, (2010) Many families of C. elegans microRNAs are not essential for development of viability. Curr Biol 20: 367-73.
3. Zhang X, Zabinsky R, Teng Y, Cui M, Han M, (2011) MicroRNAs play critical roles in the survival and recovery of Caenorhabditis elegans from starvation-induced L1 diapause. Proc Natl Acad Sci 108: 17997-8002.
4. Kudlow BA, Zhang L, Han M, (2012) Systematic analysis of tissue-restricted miRISCs reveals a broad role for microRNAs in suppressing basal activity of the C. elegans pathogen response. Mol Cell 46: 530-541.
5. 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.
6. Prasad BC, Ye B, Zackhary R, Schrader K, Seydoux G, et al. (1998) unc-3, a gene required for axonal guidance in Caenorhabditis elegans, encodes a member of the O/E family of transcription factors. Development 125: 1561-68.
7. Kim K, Colosimo ME, Yeung H, Sengupta P, (2005) The UNC-3 Olf/EBF protein represses alternate neuronal programs to specify chemosensory neuron identity. Dev Biol 286: 126-148.
8. Bargmann CI, Horvitz HR, (1991) Control of larval development by chemosensory neurons in Caenorhabditis elegans. Science 251: 1243-46.
9. Ailion M, Thomas JH, (2000) Dauer formation induced by high temperatures in Caenorhabditis elegans. Genetics 156: 1047-67.
10. Ding L, Spencer A, Morita K, Han M, (2005) The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG to cytoplasmic P bodies in C. elegans. Mol Cell 19: 437-447.
11. Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, et al. (2007) Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell 28: 598-613.
12. Von Stetina SE, Watson JD, Fox RM, Olszewski KL, Spencer WC, et al. (2007) Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. Genome Biol 8: R135.
13. McGhee JD, Birchall JC, Chung MA, Cottrell DA, Edgar LG, et al. (1990) Production of null mutants in the major intestinal esterase gene (ges-1) of the nematode Caenorhabditis elegans. Genetics 125: 505-514.
14. De Lencastre A, Pincus Z, Zhou K, Kato M, Lee SS, et al. (2010) MicroRNAs both promote and antagonize longevity in C. elegans. Curr Biol 20: 2159-2168.
15. Fielenbach N, Antebi A, (2008) C. elegans dauer formation and the molecular basis of plasticity. Genes Dev 22: 2149-2165.
16. da Graca LS, Zimmerman KK, Mitchell MC, Kozhan-Gorodetska M, Sekiewicz K, et al. (2004) DAF-5 is a ski oncoprotein homolog that functions in a neuronal TGF beta pathway to regulate C. elegans dauer development. Development 131: 435-446.
17. Larsen PL, Albert PS, Riddle DL, (1995) Genes that regulate both development and longevity in Caenorhabditis elegans. Genetics 139: 1567-83.
18. Vowels JJ, Thomas JH, (1992) Genetic analysis of chemosensory control of dauer formation in Caenorhabditis elegans. Genetics 130: 105-23.
19. Sze JY, Victor M, Loer C, Shi Y, Ruvkun G, (2000) Food and metabolism signaling defects in a serotonin-synthesis mutant. Nature 403: 560-564.
20. Liang B, Moussaif M, Kuan CJ, Gargus JJ, Sze JY, (2006) Serotonin targets the DAF-16/FOXO signaling pathway to modulate stress responses. Cell Metab 4: 429-440.
21. Daniels SA, Ailion M, Thomas JH, Sengupta P, (2000) egl-4 acts through a transforming growth factor-beta/SMAD pathway in Caenorhabditis elegans to regulate multiple neuronal circuits in response to sensory cues. Genetics 156: 123-141.
22. Zheng X, Chung S, Tanabe T, Sze JY, (2005) Cell-type specific regulation of serotonergic identity by the C. elegans LIM-homeodomain factor LIM-4. Dev Biol 286: 618-628.
23. Murakami M, Koga M, Ohshima Y, (2001) DAF-7/TGF-beta expression required for the normal larval development in C. elegans is controlled by a presumed guanylyl cyclase DAF-11. Mech Dev 109: 24-35.
24. Li W, Kennedy SG, Ruvkun G, (2003) daf-28 encodes a C. elegans insulin superfamily member that is regulated by environmental cues and acts in the DAF-2 signaling pathway. Genes Dev 17: 844-858.
25. Thomas JH, Birnby DA, Vowels JJ, (1993) Evidence for parallel processing of sensory information controlling dauer formation in Caenorhabditis elegans. Genetics 134: 1105-1117.
26. Birnby DA, Link EM, Vowels JJ, Tian H, Colacurcio PL, et al. (2000) A transmembrance guanylyl cyclase (DAF-11) and Hsp90(DAF-21) regulate a common set of chemosensory behaviors in Caenorhabditis elegans. Genetics 155: 85-104.
27. Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, et al. (2008) Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res 18: 2005-2015.
28. Johnston RJ Jr, Hobert O, (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabbaditis elegans. Nature 426: 845-849.
29. Simon DJ, Madison JM, Conery AL, Thompson-Peer KL, Soskis M, et al. (2008) The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell 133: 903-915.
30. Clark AM, Goldstein LD, Tevlin M, Tavare S, Shaham S, et al. (2010) The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nucleic Acids Res 38: 3780-3793.
31. Roy PJ, Stuart JM, Lund J, Kim SK, (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418: 975-979.
32. Pauli F, Liu Y, Kim YA, Chen PJ, Kim SK, (2006) Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans. Development 133: 287-295.
33. Jan CH, Friedman RC, Ruby JG, Bartel DP, (2011) Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs. Nature 469: 97-101.
34. Wang J, Kim SK, (2003) Global analysis of dauer gene expression in Caenorhabditis elegans. Development 130: 1621-1634.
35. Cinar H, Keles S, Jin Y, (2005) Expression profiling of GABAergic motor neurons in Caenorhabditis elegans. Curr Biol 15: 340-346.
36. Topalidou I, Chalfie M, (2011) Shared gene expression in distinct neurons expressing common selector genes. Proc Natl Acad Sci USA 108: 19258-19263.
37. van der Linden AM, Wiener S, You YJ, Kim K, Avery L, et al. (2008) The EGL-4 PKG acts with KIN-29 salt-inducible kinase and protein kinase A to regulate chemoreceptor gene expression and sensory behaviors in Caenorhabditis elegans. Genetics 180: 1475-1491.
38. 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 USA 106: 18668-18673.
39. Resnick TD, McCulloch KA, Rougvie AE, (2010) miRNAs give worms the time of their lives: small RNAs and temporal control in Caenorhabditis elegans. Dev Dyn 239: 1477-1489.
40. Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
41. Karp X, Hammell M, Ow MC, Ambros V, (2011) Effect of life history of microRNA expression during C. elegans development. RNA 17: 639-651.
42. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991-1008.