Genome-wide RNA expression profiling in rice

Rice Functional Genomics: Challenges, Progress and Prospects

Volumn , Issue , 2007, Pages 31-59

  Kikuchi, Shoshi ^a   Wang, Guo Liang ^b   Li, Lei ^c  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b OHIO STATE UNIVERSITY   (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955049659     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/0-387-48914-2_4     Document Type: Chapter

References (64)

1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter JC (1991) Complementary DNA sequencing: Expressed sequence tags and human genome project. Science 252:1651-1656.
2. Ahmad K, Henikof S (2001) Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila. Cell 104:839-847.
3. Aldaz CM (2003) Serial Analysis of Gene Expression (SAGE) in cancer research. In: Ladanyi M, Gerald W (eds) Expression profiling of human tumors: diagnostic and research applications. Humana Press, New Jersey, pp 47-60.
4. Bao J, Lee S, Chen C, Zhang X, Zhang Y, Liu S, Clark T, Wang J, Cao M, Yang H, Wang S, Yu J (2005) Serial Analysis of Gene Expression study of a hybrid rice strain (LYP9) and its parental cultivars. Plant Physiol 138:1216-1231.
5. Bennetzen JL, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128-133.
6. Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306:2242-2246.
7. Brenner S, Johnson M, Bridgham J Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr, S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630-634.
8. Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, Itoh M, Konno H, Okazaki Y, Muramatsu M, Hayashizaki Y (2000) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res 10:1617-1630.
9. Chen JJ, Rowley JD, Wang SM (2000) Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification. Proc Natl Acad Sci USA 97:349-353.
10. Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan L, Shiloff BA, Bennetzen JL (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125:1342-1353.
11. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM (1999) Expression profiling using cDNA microarrays. Nat Genet 21:10-14.
12. Ekman DR, Lorenz WW, Przybyla AE, Wolfe NL, Dean JFD (2003) SAGE analysis of transcriptome responses in Arabidopsis roots exposed to 2, 4, 6- Trinitrotoluene. Plant Physiol 133:1397-1406.
13. Fizames C, Munos S, Cazettes C, Nacry P, Boucherez J, Gaymard F, Piquemal D, Delorme V, Commes T, Doumas P, Cooke R, Marti J, Sentenac H, Gojon A (2004) The Arabidopsis root transcriptome by serial analysis of gene expression: gene identification using the genome sequence. Plant Physiol 134:67-80.
14. Gibbings JG, Cook BP, Dufault MR, Madden SL, Khuri S, Turnbull CJ, Dunwell JM (2003) Global transcript analysis of rice leaf and seed using SAGE technology. Plant Biotechnol J 1:271-285.
15. Gowda M, Jantasuriyarat C, Dean RA, Wang GL (2004) Robust-LongSAGE (RLSAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol 134:890-897.
16. Gowda M, Venu RC, Jia Y, Stahlberg E, Pampanwar V, Soderlund C, Wang GL (2007) Use of robust-long serial analysis of gene expression to identify novel fungal and plant genes involved in host-pathogen interactions. In: Ronald PC (ed) Methods Mol Biol 354:131-144.
17. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479-494.
18. Hashimoto S, Suzuki Y, Kasai Y, Morohoshi K, Yamada T, Sese J, Morishita S, Sugano S, Matsushima K (2004) 5'-end SAGE for the analysis of transcriptional start sites. Nat Biotechnol 22:1146-1149.
19. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342-347.
20. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800.
21. Jones SJ, Riddle DL, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, Stricklin SL, Baillie DL, Waterston R, Marra MA (2002) Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res 11:1346-1352.
22. Jung SH, Lee JY, Lee DH (2003) Use of SAGE technology to reveal changes in gene expression in A. thaliana leaves undergoing cold stress. Plant Mol Biol 52:553-567.
23. Kikuchi S (2007) Comprehensive analysis of rice gene expression by using the microarray system: What we have learned from the microarray project. In: Datta S (ed) Rice improvement in the genomics era. Haworth Press, Binghamton NY (In Press).
24. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A (2003) Collection, mapping, and annotation of over 28, 000 cDNA clones from japonica rice. Science 301:376-379.
25. Lee JY, Lee DH (2003) Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiol 132:517-529.
26. Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Li S, Wang J, Wang X, Deng XW (2005) Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 6:R52.
27. Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nature Genet 38:124-129.
28. Lorenz WW, Dean JF (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.
29. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309:1567-1569.
30. Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GK, Wang J, Deng XW (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15:1274-1283.
31. Maruyama K, Sugano S (1994) Oligo-capping: A simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138:171-174.
32. Matsumura H, Nirasawa S, Terauchi R (1999) Technical advance: Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J 20:719-726.
33. Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Kruger DH, Terauchi R (2003) Gene expression analysis of plant hostpathogen interactions by SuperSAGE. Proc Natl Acad Sci USA 100:15718- 15723.
34. Meyer P (2000) Transcriptional transgene silencing and chromatin components. Plant Mol Biol 43:221-234.
35. Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, Edberg SB, Ghazal H, Decola S (2004a) The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res 14:1641-1653.
36. Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild CD (2004b) Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotechnol 22:1006-1011.
37. Mockler TC, Ecker JR (2005) Applications of DNA tiling arrays for wholegenome analysis. Genomics 85:1-15.
38. Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Ridwan A, Wong CH, Liu ET, Ruan Y (2005) Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods 2:105-111.
39. Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T (2006) The rice annotation project database (RAP-DB): Hub for Oryza sativa ssp. japonica genome information. Nucl Acids Res 34:741-744.
40. Patankar S, Munasinghe A, Shoaibi A, Cummings LM, Wirth DF (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.
41. Poroyko V, Hejlek LG, Spollen WG, Springer GK, Nguyen HT, Sharp RE Bohnert HJ. (2005) The maize root transcriptome by Serial Analysis of Gene Expression. Plant Physiol 138:1700-1710.
42. Preuss D (1999) Chromatin silencing and Arabidopsis development: A role for polycomb protein. Plant Cell 11:765-767.
43. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE (2002) Using the transcriptome to annotate the genome. Nat Biotechnol 20:508-512.
44. Sasaki T, Song J, Koga-Ban Y, Matsui E, Fang F, Higo H, Nagasaki H, Hori M, Miya M, Maruyama-Kayano E, Takiguchi T, Takasuga A, Niki T, Ishimaru K, Ikeda H, Yamamoto Y, Mukai Y, Ohta I, Miyadera N, Havukkala I, Minobe Y (1994) Toward cataloguing all rice genes: Large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J 6:615- 624.
45. Sasaki T, Yano M, Kurata, N, Yamamoto K (1996) The Japanese Rice Genome Research Program. Genome Res 6:661-666.
46. Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296:141-145.
47. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 18:1262-1268.
48. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci USA 100:15776-15781.
49. Song R, Llaca V, Messing J (2002) Mosaic organization of orthologous sequences in grass genomes. Genome Res 12:1549-1555.
50. Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder1 M, Gerstein M, Wang J, Deng XW (2005) A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. Plant Mol Biol 59:137-149.
51. Tucholski J, Skowron PM, Podhajska AJ (1995) MmeI a class-IIS restriction endonuclease: Purification and characterization. Gene 157:87-92.
52. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484-487.
53. Wei CL, Ng P, Chiu KP, Wong CH, Ang CC, Lipovich L, Liu ET, Ruan Y (2004) 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci USA 101:11701-11706.
54. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T (2002) A comprehensive rice transcript map containing 6, 591 expressed sequence tag sites. Plant Cell 14:525-535.
55. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842-846.
56. Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135-144.
57. Yazaki J, Kishimoto N, Nakamura K, Fujii F, Shimbo K, Otsuka Y, Wu J, Yamamoto K, Sakata K, Sasaki T, Kikuchi S (2000) Embarking on rice functional genomics via cDNA microarray: Use of 3′ UTR probes for specific gene expression analysis. DNA Res 7:367-370.
58. Yazaki J, Kishimoto N, Ishikawa M, Kikuchi S (2002) Rice expression database: The gateway to rice functional genomics. Trends Plant Sci 7:563-564.
59. Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A, Shimbo K, Shimatani Z, Kojima K, Suzuki K, Yamamoto M, Honda S, Endo A, Yoshida Y, Sato Y, Takeuchi K, Toyoshima K, Miyamoto C, Wu J, Sasaki T, Sakata K, Yamamoto K, Iba K, Oda T, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S (2003) Genomics approach to abscisic acid- And gibberellin-responsive genes in rice. DNA Res 10:249-261.
60. Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S (2004) Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: Phenotyping and comparative analysis between rice and Arabidopsis. Physiol Genomics 17:87-100.
61. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Xiao Y, Bu D, Tan J, Yang L, Ye C, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Huang X, Su Z, Tong W, Tong Z, Ye J, Wang L, Lei T, Chen C, Chen H, Huang H, Zhang F, Li N, Zhao C, Huang Y, Li L, Xi Y, Qi Q, Li W, Hu W, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wong GK, Yang H (2005) The genomes of Oryza sativa: A history of duplications. PLoS Biol 3:E38.
62. Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR (2005) The Institute for Genomic Research Osa1 rice genome annotation database. Plant Physiol 138:18-26.
63. Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M, Wei S, Fu J, Chen Y, Ren X, Zhang Y, Ni P, Zhang J, Li S, Wang J, Wong GK, Zhao H, Yu J, Yang H, Wang J (2004) BGI-RIS: An integrated information resource and comparative analysis workbench for rice genomics. Nucl Acids Res 32:377-382.
64. Zhou Y, Tang J, Walker MG, Zhang X, Wang J, Hu S, Xu H, Deng Y, Dong J, Ye L, Lin L, Li J, Wang X, Pan Y, Lin W, Tian W, Liu J, Wei L, Liu S, Yang H, Yu J (2003) Gene identification and expression analysis of 86, 136 expressed sequence tags (EST) from the rice genome. Genomics Proteomics Bioinformatics 1:26-42.