Deep SAGE analysis of the Caenorhabditis elegans transcriptome

Nucleic Acids Research

Volumn 38, Issue 10, 2010, Pages 3252-3262

  Ruzanov, Peter ^a   Riddle, Donald L ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AAK 2; TRANSCRIPTION FACTOR CKI 1; TRANSCRIPTION FACTOR DAF 16; TRANSCRIPTION FACTOR DAF 2; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DNA SEQUENCE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE MAPPING; GENOTYPE; LARVA; LIFESPAN; LONGEVITY; NONHUMAN; PARASITE DEVELOPMENT; PRIORITY JOURNAL; RNA SPLICING; SERIAL ANALYSIS OF GENE EXPRESSION; UPREGULATION; ALTERNATIVE RNA SPLICING; ANIMAL; EVALUATION; GENE LIBRARY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY; SEQUENCE TAGGED SITE;

CAENORHABDITIS ELEGANS;

ALTERNATIVE SPLICING; ANIMALS; CAENORHABDITIS ELEGANS; GENE EXPRESSION PROFILING; GENE LIBRARY; LONGEVITY; SEQUENCE ANALYSIS, DNA; SEQUENCE TAGGED SITES;

EID: 77953699256     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq035     Document Type: Article

References (33)

1. Kulesh, D.A., Clive, D.R., Zarlenga, D.S. and Greene, J.J. (1987) Identification of interferon-modulated proliferation-related cDNA sequences. Proc. Natl Acad. Sci. USA, 84, 8453-8457.
2. Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
3. Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
4. Ibrahim, A.F., Hedley, P.E., Cardle, L., Kruger, W., Marshall, D.F., Muehlbauer, G.J. and Waugh, R. (2005) A comparative analysis of transcript abundance using SAGE and Affymetrix arrays. Funct. Integr. Genomics, 5, 163-174.
5. Sun, M., Zhou, G., Lee, S., Chen, J., Shi, R.Z. and Wang, S.M. (2004) SAGE is far more sensitive than EST for detecting low-abundance transcripts. BMC Genomics, 5, 1.
6. Vilain, C., Libert, F., Venet, D., Costagliola, S. and Vassart, G. (2003) Small amplified RNA-SAGE: an alternative approach to study transcriptome from limiting amount of mRNA. Nucleic Acids Res., 31, e24.
7. Morrissy, A., Morin, R., Delaney, A., Zeng, T., McDonald, H., Zhao, Y., Jones, S., Hirst, M. and Marra, M. (2009) Next-generation tag sequencing for cancer gene expression profiling. Genome Res., 19, 1825-1835.
8. Kim, J.B., Porreca, G.J., Song, L., Greenway, S.C., Gorham, J.M., Church, G.M., Seidman, C.E. and Seidman, J.G. (2007) Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science, 316, 1481-1484.
9. Morin, R., Bainbridge, M., Fejes, A., Hirst, M., Krzywinski, M., Pugh, T., McDonald, H., Varhol, R., Jones, S. and Marra, M. (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques, 45, 81-94.
10. Kenyon, C., Chang, J., Gensch, E., Rudner, A. and Tabtiang, R. (1993) A C.elegans mutant that lives twice as long as wild type. Nature, 366, 461-464.
11. Kimura, K.D., Tissenbaum, H.A., Liu, Y. and Ruvkun, G. (1997) daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. Science, 277, 942-946.
12. Halaschek-Wiener, J., Khattra, J.S., McKay, S., Pouzyrev, A., Stott, J.M., Yang, G.S., Holt, R.A., Jones, S.J., Marra, M.A., Brooks-Wilson, A.R. et al. (2005) Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res., 15, 603-615.
13. Ruzanov, P., Riddle, D.L., Marra, M.A., McKay, S.J. and Jones, S.M. (2007) Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Exp. Gerontol., 42, 825-839.
14. Golden, J.W. and Riddle, D.L. (1984) The Caenorhabditis elegans dauer larva: developmental effects of pheromone, food, and temperature. Dev. Biol., 102, 368-378.
15. Holt, S.J. and Riddle, D.L. (2003) SAGE surveys C. elegans carbohydrate metabolism: evidence for an anaerobic shift in the long-lived dauer larva. Mech. Ageing Dev., 124, 779-800.
16. Jones, S.J., Riddle, D.L., Pouzyrev, A.T., Velculescu, V.E., Hillier, L., Eddy, S.R., Stricklin, S.L., Baillie, D.L., Waterston, R. and Marra, M.A. (2001) Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res., 11, 1346-1352.
17. McKay, S.J., Johnsen, R., Khattra, J., Asano, J., Baillie, D.L., Chan, S., Dube, N., Fang, L., Goszczynski, B., Ha, E. et al. (2003) Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harb. Symp. Quant. Biol., 68, 159-169.
18. Pleasance, E.D., Marra, M.A. and Jones, S.J. (2003) Assessment of SAGE in transcript identification. Genome Res., 13, 1203-1215.
19. Khattra, J., Delaney, A.D., Zhao, Y., Siddiqui, A., Asano, J., McDonald, H., Pandoh, P., Dhalla, N., Prabhu, A.L., Ma, K. et al. (2007) Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res., 17, 108-116.
20. Dennis, G.J., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. and Lempicki, R.A. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol., 4, P3.
21. Flicek, P., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T. et al. (2008) Ensembl 2008. Nucleic Acids Res., 36, D707-D714.
22. McElwee, J.J., Schuster, E., Blanc, E., Thomas, J.H. and Gems, D. (2004) Shared transcriptional signature in Caenorhabditis elegans dauer larvae and long-lived daf-2 mutants implicates detoxification system in longevity assurance. J. Biol. Chem., 279, 44533-44543.
23. Hillier, L.W., Marth, G.T., Quinlan, A.R., Dooling, D., Fewell, G., Barnett, D., Fox, P., Glasscock, J.I., Hickenbotham, M., Huang, W. et al. (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods, 5, 183-188.
24. Baugh, L.R. and Sternberg, P.W. (2006) DAF-16/FOXO regulates transcription of cki-1/Cip/Kip and repression of lin-4 during C. elegans L1 arrest. Curr. Biol., 16, 780-785.
25. Henderson, S.T., Bonafè, M. and Johnson, T.E. (2006) daf-16 protects the nematode Caenorhabditis elegans during food deprivation. J. Gerontol. A Biol. Sci. Med. Sci., 61, 444-460.
26. The Gene Ontology Consortium. (2000) Gene Ontology: tool for the unification of biology. Nature Genetics, 25, 25-29.
27. Gunasekera, A.M., Patankar, S., Schug, J., Eisen, G., Kissinger, J., Roos, D. and Wirth, D.F. (2004) Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Mol. Biochem. Parasitol., 136, 35-42.
28. Patankar, S., Munasinghe, A., Shoaibi, A., Cummings, L.M. and Wirth, D.F. (2001) Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite. Mol. Biol. Cell, 12, 3114-3125.
29. Kuo, B.Y., Chen, Y., Bohacec, S., Johansson, O., Wasserman, W.W. and Simpson, E.M. (2006) SAGE2Splice: unmapped SAGE tags reveal novel splice junctions. PLoS Comput. Biol., 2, e34.
30. Ruzanov, P., Jones, S.J. and Riddle, D.L. (2007) Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data. BMC Genomics, 8, 447.
31. Vanfleteren, J.R. and De Vreese, A. (1995) The gerontogenes age-1 and daf-2 determine metabolic rate potential in aging Caenorhabditis elegans. FASEB J., 9, 1355-1361.
32. Perez, V.I., Bokov, A., Remmen, H.V., Mele, J., Ran, Q., Ikeno, Y. and Richardson, A. (2009) Is the oxidative stress theory of aging dead? Biochim. Biophys. Acta, 1790, 1005-1014.
33. Van Raamsdonk, J.M. and Hekimi, S. (2009) Deletion of the mitochondrial superoxide dismutase sod-2 extends lifespan in Caenorhabditis elegans. PLoS Genet., 5, e1000361.