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Volumn 2, Issue 3, 2007, Pages

Global identification and characterization of transcriptionally active regions in the rice genome

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; COMPLEMENTARY DNA; PLANT DNA; PLANT RNA;

EID: 34447107819     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000294     Document Type: Article
Times cited : (71)

References (48)
  • 1
    • 0037023349 scopus 로고    scopus 로고
    • A draft sequence of the rice genome (Oryza sativa L. ssp japonica)
    • Goff SA, Ricke D, Lan TH, Presting G, Wang R, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296: 92-100.
    • (2002) Science , vol.296 , pp. 92-100
    • Goff, S.A.1    Ricke, D.2    Lan, T.H.3    Presting, G.4    Wang, R.5
  • 2
    • 0037023384 scopus 로고    scopus 로고
    • A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
    • Yu J, Hu S, Wang J, Wong GK, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
    • (2002) Science , vol.296 , pp. 79-92
    • Yu, J.1    Hu, S.2    Wang, J.3    Wong, G.K.4    Li, S.5
  • 3
    • 20144366003 scopus 로고    scopus 로고
    • The genomes of Oryza sativa: A history of duplications
    • Yu J, Wang J, Lin W, Li S, Li H, et al. (2005) The genomes of Oryza sativa: A history of duplications. PLOS Biol 3: e38.
    • (2005) PLOS Biol , vol.3
    • Yu, J.1    Wang, J.2    Lin, W.3    Li, S.4    Li, H.5
  • 4
    • 0037153190 scopus 로고    scopus 로고
    • The genome sequence and structure of rice chromosome 1
    • Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, et al. (2002) The genome sequence and structure of rice chromosome 1. Nature 420: 312-316.
    • (2002) Nature , vol.420 , pp. 312-316
    • Sasaki, T.1    Matsumoto, T.2    Yamamoto, K.3    Sakata, K.4    Baba, T.5
  • 5
    • 0037153127 scopus 로고    scopus 로고
    • Sequence and analysis of rice chromosome 4
    • Feng Q, Zhang Y, Hao P, Wang S, Fu G, et al. (2002) Sequence and analysis of rice chromosome 4. Nature 420: 316-320.
    • (2002) Nature , vol.420 , pp. 316-320
    • Feng, Q.1    Zhang, Y.2    Hao, P.3    Wang, S.4    Fu, G.5
  • 6
    • 0038581538 scopus 로고    scopus 로고
    • In-depth view of structure, activity, and evolution of rice Chromosome 10
    • The Rice Chromosome 10 Sequencing Consortium
    • The Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice Chromosome 10. Science 300: 1566-1569.
    • (2003) Science , vol.300 , pp. 1566-1569
  • 7
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • International Rice Genome Sequencing Project
    • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
    • (2005) Nature , vol.436 , pp. 793-800
  • 8
    • 25444470149 scopus 로고    scopus 로고
    • The institute for genomic research osa1 rice genome annotation database
    • Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, et al. (2005) The institute for genomic research osa1 rice genome annotation database. Plant Physiol 138: 18-26.
    • (2005) Plant Physiol , vol.138 , pp. 18-26
    • Yuan, Q.1    Ouyang, S.2    Wang, A.3    Zhu, W.4    Maiti, R.5
  • 9
    • 26444618382 scopus 로고    scopus 로고
    • Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice
    • Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 300: 1566-1569.
    • (2003) Science , vol.300 , pp. 1566-1569
    • Kikuchi, S.1    Satoh, K.2    Nagata, T.3    Kawagashira, N.4    Doi, K.5
  • 10
    • 85142157291 scopus 로고    scopus 로고
    • Juretic N, Bureau TE, Bruskiewich RM (2004) Transposable element annotation of the rice genome. Bioinformatics 20: 155-160.
    • Juretic N, Bureau TE, Bruskiewich RM (2004) Transposable element annotation of the rice genome. Bioinformatics 20: 155-160.
  • 11
    • 0033375845 scopus 로고    scopus 로고
    • Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE)
    • Matsumura H, Nirasawa S, Terauchi R (1999) Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J 20: 719-726.
    • (1999) Plant J , vol.20 , pp. 719-726
    • Matsumura, H.1    Nirasawa, S.2    Terauchi, R.3
  • 12
    • 33644876658 scopus 로고    scopus 로고
    • Plant MPSS databases: Signature-based transcriptional resources for analyses of mRNA and small RNA
    • Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, et al. (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 34: D731-D735.
    • (2006) Nucleic Acids Res , vol.34
    • Nakano, M.1    Nobuta, K.2    Vemaraju, K.3    Tej, S.S.4    Skogen, J.W.5
  • 13
    • 33744534995 scopus 로고    scopus 로고
    • SuperSAGE array: The direct use of 26-base-pair transcript tags in oligonucleotide arrays
    • Matsumura H, Bin Nasir KH, Yoshida K, Ito A, Kahl G, et al. (2006) SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Methods 3: 469-474.
    • (2006) Nat Methods , vol.3 , pp. 469-474
    • Matsumura, H.1    Bin Nasir, K.H.2    Yoshida, K.3    Ito, A.4    Kahl, G.5
  • 14
    • 33646932116 scopus 로고    scopus 로고
    • Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture
    • Li L, Wang X, Xia M, Stolc V, Su N, et al. (2005) Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 6: R52.
    • (2005) Genome Biol , vol.6
    • Li, L.1    Wang, X.2    Xia, M.3    Stolc, V.4    Su, N.5
  • 15
    • 29444438757 scopus 로고    scopus 로고
    • Genome-wide transcription analyses in rice using tiling microarrays
    • Li L, Wang X, Stolc V, Li X, Zhang D, et al. (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38: 124-129.
    • (2006) Nat Genet , vol.38 , pp. 124-129
    • Li, L.1    Wang, X.2    Stolc, V.3    Li, X.4    Zhang, D.5
  • 16
    • 10644247621 scopus 로고    scopus 로고
    • Applications of DNA tiling arrays for whole-genome analysis
    • Mockler TC, Ecker JR (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85: 1-15.
    • (2005) Genomics , vol.85 , pp. 1-15
    • Mockler, T.C.1    Ecker, J.R.2
  • 17
    • 12344291073 scopus 로고    scopus 로고
    • Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments
    • Johnson JM, Edwards S, Shoemaker D, Schadt EE (2005) Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet 21: 93-102.
    • (2005) Trends Genet , vol.21 , pp. 93-102
    • Johnson, J.M.1    Edwards, S.2    Shoemaker, D.3    Schadt, E.E.4
  • 18
    • 0035072249 scopus 로고    scopus 로고
    • Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer
    • Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19: 342-347.
    • (2001) Nat Biotechnol , vol.19 , pp. 342-347
    • Hughes, T.R.1    Mao, M.2    Jones, A.R.3    Burchard, J.4    Marton, M.J.5
  • 19
    • 0032846163 scopus 로고    scopus 로고
    • Maskless fabrication of light-directed oligonucleotide microarrays using a digital micro-mirror array
    • Singh-Gasson S, Green RD, Yue YJ, Nelson C, Blattner F, et al. (1999) Maskless fabrication of light-directed oligonucleotide microarrays using a digital micro-mirror array. Nat Biotechnol 17: 974-978.
    • (1999) Nat Biotechnol , vol.17 , pp. 974-978
    • Singh-Gasson, S.1    Green, R.D.2    Yue, Y.J.3    Nelson, C.4    Blattner, F.5
  • 20
    • 0242300620 scopus 로고    scopus 로고
    • Empirical analysis of transcriptional activity in the Arabidopsis genome
    • Yamada K, Lim J, Dale JM, Chen H, Shinn P, et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: 842-846.
    • (2003) Science , vol.302 , pp. 842-846
    • Yamada, K.1    Lim, J.2    Dale, J.M.3    Chen, H.4    Shinn, P.5
  • 21
    • 0035865260 scopus 로고    scopus 로고
    • Experimental annotation of the human genome using microarray technology
    • Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, et al. (2001) Experimental annotation of the human genome using microarray technology. Nature 409: 922-927.
    • (2001) Nature , vol.409 , pp. 922-927
    • Shoemaker, D.D.1    Schadt, E.E.2    Armour, C.D.3    He, Y.D.4    Garrett-Engele, P.5
  • 22
    • 0033664358 scopus 로고    scopus 로고
    • RNA expression analysis using a 30 base pair resolution Escherichia coli genome array
    • Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, et al. (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnol 18: 1262-1268.
    • (2000) Nature Biotechnol , vol.18 , pp. 1262-1268
    • Selinger, D.W.1    Cheung, K.J.2    Mei, R.3    Johansson, E.M.4    Richmond, C.S.5
  • 24
    • 19944376457 scopus 로고    scopus 로고
    • Global identification of human transcribed sequences with genome tiling arrays
    • Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246.
    • (2004) Science , vol.306 , pp. 2242-2246
    • Bertone, P.1    Stolc, V.2    Royce, T.E.3    Rozowsky, J.S.4    Urban, A.E.5
  • 25
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    • Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-1154.
    • (2005) Science , vol.308 , pp. 1149-1154
    • Cheng, J.1    Kapranov, P.2    Drenkow, J.3    Dike, S.4    Brubaker, S.5
  • 26
    • 7444233156 scopus 로고    scopus 로고
    • A gene expression map for the euchromatic genome of Drosophila melanogaster
    • Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, et al. (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306: 655-660.
    • (2004) Science , vol.306 , pp. 655-660
    • Stolc, V.1    Gauhar, Z.2    Mason, C.3    Halasz, G.4    van Batenburg, M.F.5
  • 27
    • 0141905891 scopus 로고    scopus 로고
    • Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    • Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31: 5654-5666.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5654-5666
    • Haas, B.J.1    Delcher, A.L.2    Mount, S.M.3    Wortman, J.R.4    Smith, R.K.5
  • 28
    • 20844441941 scopus 로고    scopus 로고
    • Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)
    • Kitagawa N, Washio T, Kosugi S, Yamashita T, Higashi K, et al. (2005) Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics 21: 1758-1763.
    • (2005) Bioinformatics , vol.21 , pp. 1758-1763
    • Kitagawa, N.1    Washio, T.2    Kosugi, S.3    Yamashita, T.4    Higashi, K.5
  • 29
    • 0025721986 scopus 로고
    • Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA
    • Munroe SH, Lazar MA (1991) Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem 266: 22083-22086.
    • (1991) J Biol Chem , vol.266 , pp. 22083-22086
    • Munroe, S.H.1    Lazar, M.A.2
  • 30
    • 0028854931 scopus 로고
    • Naturally occurring antisense transcripts are present in chick embryo chondrocytes simultaneously with the down-regulation of the alpha 1 (I) collagen gene
    • Farrell CM, Lukens LN (1995) Naturally occurring antisense transcripts are present in chick embryo chondrocytes simultaneously with the down-regulation of the alpha 1 (I) collagen gene. J Biol Chem 270: 3400-3408.
    • (1995) J Biol Chem , vol.270 , pp. 3400-3408
    • Farrell, C.M.1    Lukens, L.N.2
  • 31
    • 0032932528 scopus 로고    scopus 로고
    • Tsix, a gene antisense to Xist at the X-inactivation centre
    • Lee JT, Davidow LS, Warshawsky D (1999) Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 21: 400-404.
    • (1999) Nat Genet , vol.21 , pp. 400-404
    • Lee, J.T.1    Davidow, L.S.2    Warshawsky, D.3
  • 32
    • 4644312235 scopus 로고    scopus 로고
    • The role of RNA interference in heterochromatic silencing
    • Lippman Z, Martienssen RA (2004) The role of RNA interference in heterochromatic silencing. Nature 431: 364-370.
    • (2004) Nature , vol.431 , pp. 364-370
    • Lippman, Z.1    Martienssen, R.A.2
  • 33
    • 29244490062 scopus 로고    scopus 로고
    • Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
    • Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123: 1279-1291.
    • (2005) Cell , vol.123 , pp. 1279-1291
    • Borsani, O.1    Zhu, J.2    Verslues, P.E.3    Sunkar, R.4    Zhu, J.K.5
  • 34
    • 33745804463 scopus 로고    scopus 로고
    • MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by Argonaute, Dicer, and RNA-dependent RNA polymerase in Arabidopsis
    • Ronemus M, Vaughn MW, Martienssen RA (2006) MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by Argonaute, Dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell 18: 1559-1574.
    • (2006) Plant Cell , vol.18 , pp. 1559-1574
    • Ronemus, M.1    Vaughn, M.W.2    Martienssen, R.A.3
  • 36
    • 12244275645 scopus 로고    scopus 로고
    • Widespread occurrence of antisense transcription in the human genome
    • Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, et al. (2003) Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 21: 379-386.
    • (2003) Nat Biotechnol , vol.21 , pp. 379-386
    • Yelin, R.1    Dahary, D.2    Sorek, R.3    Levanon, E.Y.4    Goldstein, O.5
  • 37
    • 24644448635 scopus 로고    scopus 로고
    • Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana
    • Wang XJ, Gaasterland T, Chua NH (2005) Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol 6: R30.
    • (2005) Genome Biol , vol.6
    • Wang, X.J.1    Gaasterland, T.2    Chua, N.H.3
  • 39
    • 4944239027 scopus 로고    scopus 로고
    • Pack-MULE transposable elements mediate gene evolution in plants
    • Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431: 569-573.
    • (2004) Nature , vol.431 , pp. 569-573
    • Jiang, N.1    Bao, Z.2    Zhang, X.3    Eddy, S.R.4    Wessler, S.R.5
  • 40
    • 24344459435 scopus 로고    scopus 로고
    • Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res 15: 1292-1297.
    • Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res 15: 1292-1297.
  • 41
    • 33845395154 scopus 로고    scopus 로고
    • Prediction of trans-antisense transcripts in Arabidopsis thaliana
    • Wang H, Chua NH, Wang XJ (2006) Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biol 7: R92.
    • (2006) Genome Biol , vol.7
    • Wang, H.1    Chua, N.H.2    Wang, X.J.3
  • 43
    • 30044435097 scopus 로고    scopus 로고
    • Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression
    • Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, et al. (2006) Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. Genome Res 16: 20-29.
    • (2006) Genome Res , vol.16 , pp. 20-29
    • Deng, W.1    Zhu, X.2    Skogerbo, G.3    Zhao, Y.4    Fu, Z.5
  • 45
    • 0000663168 scopus 로고
    • An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae
    • Kauffman HE, Reddy APK, Hsieh SPY, Merca SD (1973) An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Dis Rep 57: 537-541.
    • (1973) Plant Dis Rep , vol.57 , pp. 537-541
    • Kauffman, H.E.1    Reddy, A.P.K.2    Hsieh, S.P.Y.3    Merca, S.D.4
  • 46
    • 0038239283 scopus 로고    scopus 로고
    • OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
    • Rouillard JM, Zuker M, Gulari E (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res 31: 3057-3062.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3057-3062
    • Rouillard, J.M.1    Zuker, M.2    Gulari, E.3
  • 47
    • 22144467302 scopus 로고    scopus 로고
    • Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    • Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, et al. (2005) Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet 21: 466-475.
    • (2005) Trends Genet , vol.21 , pp. 466-475
    • Royce, T.E.1    Rozowsky, J.S.2    Bertone, P.3    Samanta, M.4    Stolc, V.5
  • 48
    • 33751356200 scopus 로고    scopus 로고
    • NMPP: A user-customized NimbleGen microarray data processing pipeline
    • Wang X, He H, Li L, Chen R, Deng XW, et al. (2006) NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics 22: 2955-2957.
    • (2006) Bioinformatics , vol.22 , pp. 2955-2957
    • Wang, X.1    He, H.2    Li, L.3    Chen, R.4    Deng, X.W.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.