Global transcript analysis of rice leaf and seed using SAGE technology

Plant Biotechnology Journal

Volumn 1, Issue 4, 2003, Pages 271-285

  Gibbings, J George ^a   Cook, Brian P ^b   Dufault, Michael R ^b   Madden, Stephen L ^b   Khuri, Sawsan ^a   Turnbull, Chris J ^a   Dunwell, Jim M ^a  

^a UNIVERSITY OF READING   (United Kingdom)

^b GENZYME CORPORATION   (United States)

Author keywords

antisense; leaf; rice; SAGE; seed; transcript

Indexed keywords

EID: 1642563198     PISSN: 14677644     EISSN: 14677652     Source Type: Journal    
DOI: 10.1046/j.1467-7652.2003.00026.x     Document Type: Article

References (48)

1. Abdullah, S.N.A., Cheah, S.C. and Murphy, D.J. (2002) Isolation and characterisation of two divergent type 3 metallothioneins from oil palm, Elaeis guineensis. Plant Physiol. Biochem. 40, 255–263.
2. Anderson, L. and Seilhamer, J. (1997) A comparison of selected mRNA and protein abundances in human liver. Electrophoresis, 18, 533–537.pmid/9150937
3. Anisimov, S.V., Tarasov, K.V., Tweedie, D., Stern, M.D., Wobus, A.M. and Boheler, K.R. (2002) SAGE identification of gene transcripts with profiles unique to pluripotent mouse R1 embryonic stem cells. Genomics, 79, 169–176.pmid/11829487
4. Ansaldi, R., Chaboud, A. and Dumas, C. (2000) Multiple S gene family members including natural antisense transcripts are differentially expressed during development of maize flowers. J. Biol. Chem. 275, 24146–24155.pmid/10821836
5. Brkljacic, J.M., Maksimovic, V.R., Radovic, S.R. and Savic, A.P. (1999) Isolation of metallothionein-like cDNA clone from buckwheat. J. Plant Physiol. 154, 802–804.
6. Buchholz, W.G., Harrishaller, L., Derose, R.T. and Hall, T.C. (1994) Cyclophilins are encoded by a small gene family in rice. Plant Mol. Biol. 25, 837–843.pmid/8075400
7. Caron, H., Van Schaik, B., Van Der Mee, M., Baas, F., Riggins, G., Van Sluis, P., Hermus, M.C., Van Asperen, R., Boon, K., Voute, P.A. et al. (2001) The human transcriptome map: Clustering of highly expressed genes in chromosomal domains. Science, 291, 1289–1292.pmid/11181992
8. Chirico, W.J., Waters, M.G. and Blobel, G. (1988) 70k heat-shock related proteins stimulate protein translocation into microsomes. Nature, 332, 805–810.pmid/3282179
9. Dunwell, J.M. (2002) Future prospects for transgenic crops. Phytochem. Rev. 1, 1–12.
10. Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X. et al. (2002) Sequence and analysis of rice chromosome 4. Nature, 420, 316–320.pmid/12447439
11. Gale, M.D. (1998) Plant comparative genetics after 10 years. Science, 282, 656–659.pmid/9784118
12. Garcia-Hernandez, M., Murphy, A. and Taiz, L. (1998) Metallothioneins 1 and 2 have distinct but overlapping expression patterns in Arabidopsis. Plant Physiol. 118, 387–397.pmid/9765524
13. Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R.L., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92–100.pmid/11935018
14. Gygi, S.P., Rochon, Y., Franza, B.R. and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720–1730.pmid/10022859
15. Hashimoto, S., Suzuki, T., Dong, H.Y., Nagai, S., Yamazaki, N. and Matsushima, K. (1999) Serial analysis of gene expression in human monocyte-derived dendritic cells. Blood, 94, 845–852.pmid/10419874
16. Hibi, K., Liu, Q., Beaudry, G.A., Madden, S.L., Westra, W.H., Wehage, S.L., Yang, S.C., Heitmiller, R.F., Bertelsen, A.H., Sidransky, D. et al. (1998) Serial analysis of gene expression in non-small cell lung cancer. Cancer Res. 58, 5690–5694.pmid/9865724
17. Hsieh, H.M., Liu, W.K., Chang, A. and Huang, P.C. (1996) RNA expression patterns of a type 2 metallothionein-like gene from rice. Plant Mol. Biol. 32, 525–529.pmid/8980501
18. Hsieh, H.M., Liu, W.K. and Huang, P.C. (1995) A novel stress-inducible metallothionein-like gene from rice. Plant Mol. Biol. 28, 381–389.pmid/7632910
19. Inoue, H., Sawada, M., Ryo, A., Tanahashi, H., Wakatsuki, T., Hada, A., Kondoh, N., Nakagaki, K., Takahashi, K., Suzumura, A. et al. (1999) Serial analysis of gene expression in a microglial cell line. Glia, 28, 265–271.pmid/10559785
20. Jasper, H., Benes, V., Schwager, C., Sauer, S., Clauder-Munster, S., Ansorge, W. and Bohmann, D. (2001) The genomic response of the Drosophila embryo to JNK signaling. Dev. Cell. 1, 579–586.pmid/11703947
21. Jones, S.J.M., 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.pmid/11483575
22. Kagi, J.H.R. and Schaffer, A. (1988) Biochemistry of metallothionein. Biochemistry, 27, 8509–8515.pmid/3064814
23. Kal, A.J., Van Zonneveld, A.J., Benes, V., Van Den Berg, M., Koerkamp, M.G., Albermann, K., Strack, N., Ruijter, J.M., Richter, A., Dujon, B. et al. (1999) Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol. Biol. Cell. 10, 1859–1872.pmid/10359602
24. Kim, W.T., Li, X.X. and Okita, T.W. (1993) Expression of storage protein multigene families in developing rice endosperm. Plant Cell Physiol. 34, 595–603.
25. Liu, J.Y., Hara, C., Umeda, M., Zhao, Y., Okita, T.W. and Uchimiya, H. (1995) Analysis of randomly isolated cDNAs from developing endosperm of rice (Oryza sativa L): Evaluation of expressed sequence tags, and expression levels of mRNAs. Plant Mol. Biol. 29, 685–689.pmid/8541495
26. Lorenz, W.W. and Dean, J.F.D. (2002) SAGE profiling and demonstration of differential gene expression along the axial developmental gradient of lignifying xylem in loblolly pine (Pinus taeda). Tree Physiol. 22, 301–310.pmid/11960754
27. Matsumura, H., Nirasawa, S. and Terauchi, R. (1999) Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J. 20, 719–726.pmid/10652144
28. Moriguchi, T., Kita, M., Hisada, S., Endo-Inagaki, T. and Omura, M. (1998) Characterization of gene repertoires at mature stage of citrus fruits through random sequencing and analysis of redundant metallothionein-like genes expressed during fruit development. Gene, 211, 221–227.pmid/9602134
29. Murphy, A., Zhou, J.M., Goldsbrough, P.B. and Taiz, L. (1997) Purification and immunological identification of metallothioneins 1 and 2 from Arabidopsis thaliana. Plant Physiol. 113, 1293–1301.pmid/9112777
30. Neilson, L., Andalibi, A., Kang, D., Coutifaris, C., Strauss, J.F., Stanton, J.A.L. and Green, D.P.L. (2000) Molecular phenotype of the human oocyte by PCR-SAGE. Genomics, 63, 13–24.pmid/10662540
31. 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.pmid/11598196
32. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y. et al. (2002) The genome sequence and structure of rice chromosome 1. Nature, 420, 312–316.pmid/12447438
33. Schaffrath, U., Zabbai, F. and Dudler, R. (2000) Characterization of RCI-1, a chloroplastic rice lipoxygenase whose synthesis is induced by chemical plant resistance activators. Eur. J. Biochem. 267, 5935–5942.pmid/10998053
34. Shotwell, M.A., Boyer, S.K., Chesnut, R.S. and Larkins, B.A. (1990) Analysis of seed storage protein genes of oats. J. Biol. Chem. 265, 9652–9658.pmid/2351662
35. Spena, A., Krause, E. and Dobberstein, B. (1985) Translation efficiency of Zein messenger-RNA is reduced by hybrid formation between the 5′-untranslated and 3′-untranslated region. EMBO J. 4, 2153–2158.
36. Takaiwa, F. (1998) Structure and expression of rice seed storage protein genes. In: Molecular Biology of Rice (Shimamoto, K., ed.), pp. 179–199. Heidelburg: Springer.
37. Terryn, N. and Rouze, P. (2000) The sense of naturally transcribed antisense RNAs in plants. Trends Plant Sci. 5, 394–396.pmid/10973095
38. Thomas, S.W., Glaring, M.A., Rasmussen, S.W., Kinane, J.T. and Oliver, R.P. (2002) Transcript profiling in the barley mildew pathogen Blumeria graminis by serial analysis of gene expression (SAGE). Mol. Plant-Microbe Interact. 15, 847–856.pmid/12182343
39. Trendelenburg, G., Prass, K., Priller, J., Kapinya, K., Polley, A., Muselmann, C., Ruscher, K., Kannbley, U., Schmitt, A.O., Castell, S. et al. (2002) Serial analysis of gene expression identifies metallothionein-II as major neuroprotective gene in mouse focal cerebral ischemia. J. Neurosci. 22, 5879–5888.pmid/12122050
40. Van Breusegem, F., Dekeyser, R., Garcia, A.B., Claes, B., Gielen, J., Vanmontagu, M. and Caplan, A.B. (1994) Heat-inducible rice hsp82 and hsp70 are not always coregulated. Planta, 193, 57–66.pmid/7764623
41. Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995) Serial analysis of gene-expression. Science, 270, 484–487.pmid/7570003
42. Velculescu, V.E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett, D.E., Hieter, P., Vogelstein, B. and Kinzler, K.W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243–251.pmid/9008165
43. Virlon, B., Cheval, L., Buhler, J.M., Billon, E., Doucet, A. and Elalouf, J.M. (1999) Serial microanalysis of renal transcriptomes. Proc. Natl Acad. Sci. USA, 96, 15286–15291.pmid/10611377
44. Welle, S., Bhatt, K. and Thornton, C.A. (1999) Inventory of high-abundance mRNAs in skeletal muscle of normal men. Genome Res. 9, 506–513.pmid/10330131
45. Wong, G.K.S., Wang, J., Tao, L., Tan, J., Zhang, J.G., Passey, D.A. and Yu, J. (2002) Compositional gradients in Gramineae genes. Genome Res. 12, 851–856.pmid/12045139
46. Yamashita, T., Hashimoto, S., Kaneko, S., Nagai, S., Toyoda, N., Suzuki, T., Kobayashi, K. and Matsushima, K. (2000) Comprehensive gene expression profile of a normal human liver. Biochem. Biophys. Res. Comm. 269, 110–116.pmid/10694486
47. Yu, J., Hu, S.N., Wang, J., Wong, G.K.S., Li, S.G., Liu, B., Deng, Y.J., Dai, L., Zhou, Y., Zhang, X.Q. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79–92.pmid/11935017
48. Yu, L.H., Umeda, M., Liu, J.Y., Zhao, N.M. and Uchimiya, H. (1998) A novel MT gene of rice plants is strongly expressed in the node portion of the stem. Gene, 206, 29–35.pmid/9461411