메뉴 건너뛰기




Volumn 9, Issue 6, 2014, Pages

Complex interplay among DNA modification, noncoding RNA expression and protein-coding RNA expression in Salvia miltiorrhiza chloroplast genome

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; GENOMIC DNA; TRANSCRIPTOME; UNTRANSLATED RNA; MESSENGER RNA; PLANT DNA; PLANT RNA;

EID: 84902687784     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099314     Document Type: Article
Times cited : (22)

References (43)
  • 1
    • 27844511101 scopus 로고    scopus 로고
    • Danshen: An overview of its chemistry, pharmacology, pharmacokinetics, and clinical use
    • DOI 10.1177/0091270005282630
    • Zhou L, Zuo Z, Chow MS (2005) Danshen: an overview of its chemistry, pharmacology, pharmacokinetics, and clinical use. J Clin Pharmacol 45: 1345-1359. (Pubitemid 41643896)
    • (2005) Journal of Clinical Pharmacology , vol.45 , Issue.12 , pp. 1345-1359
    • Zhou, L.1    Zuo, Z.2    Chow, M.S.S.3
  • 2
    • 60649119124 scopus 로고    scopus 로고
    • Advancement in analysis of Salviae miltiorrhizae Radix et Rhizoma (Danshen)
    • Li YG, Song L, Liu M, Hu ZB, Wang ZT (2009) Advancement in analysis of Salviae miltiorrhizae Radix et Rhizoma (Danshen). J Chromatogr A 1216: 1941-1953.
    • (2009) J Chromatogr A , vol.1216 , pp. 1941-1953
    • Li, Y.G.1    Song, L.2    Liu, M.3    Hu, Z.B.4    Wang, Z.T.5
  • 3
    • 80053316627 scopus 로고    scopus 로고
    • De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients
    • Wenping H, Yuan Z, Jie S, Lijun Z, Zhezhi W (2011) De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients. Genomics 98: 272-279.
    • (2011) Genomics , vol.98 , pp. 272-279
    • Wenping, H.1    Yuan, Z.2    Jie, S.3    Lijun, Z.4    Zhezhi, W.5
  • 4
    • 37249014420 scopus 로고    scopus 로고
    • Chloroplast vector systems for biotechnology applications
    • DOI 10.1104/pp.107.106690
    • Verma D, Daniell H (2007) Chloroplast vector systems for biotechnology applications. Plant Physiol 145: 1129-1143. (Pubitemid 350276732)
    • (2007) Plant Physiology , vol.145 , Issue.4 , pp. 1129-1143
    • Verma, D.1    Daniell, H.2
  • 5
    • 0037213560 scopus 로고    scopus 로고
    • Chloroplast research in the genomic age
    • Leister D (2003) Chloroplast research in the genomic age. Trends Genet 19: 47-56.
    • (2003) Trends Genet , vol.19 , pp. 47-56
    • Leister, D.1
  • 6
    • 0026860017 scopus 로고
    • The chloroplast genome
    • Sugiura M (1992) The chloroplast genome. Plant Mol Biol 19: 149-168.
    • (1992) Plant Mol Biol , vol.19 , pp. 149-168
    • Sugiura, M.1
  • 8
    • 42449103989 scopus 로고    scopus 로고
    • Coordination of gene expression between organellar and nuclear genomes
    • DOI 10.1038/nrg2348, PII NRG2348
    • Woodson JD, Chory J (2008) Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 9: 383-395. (Pubitemid 351559601)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.5 , pp. 383-395
    • Woodson, J.D.1    Chory, J.2
  • 9
    • 84874539448 scopus 로고    scopus 로고
    • The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza
    • Qian J, Song J, Gao H, Zhu Y, Xu J, et al. (2013) The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza . PLoS One 8: e57607.
    • (2013) PLoS One , vol.8
    • Qian, J.1    Song, J.2    Gao, H.3    Zhu, Y.4    Xu, J.5
  • 10
    • 84869092510 scopus 로고    scopus 로고
    • Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome
    • Bethesda
    • Hotto AM, Schmitz RJ, Fei Z, Ecker JR, Stern DB (2011) Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome. G3 (Bethesda) 1: 559-570.
    • (2011) G3 , vol.1 , pp. 559-570
    • Hotto, A.M.1    Schmitz, R.J.2    Fei, Z.3    Ecker, J.R.4    Stern, D.B.5
  • 11
    • 61449126060 scopus 로고    scopus 로고
    • Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
    • Ben Amor B, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, et al. (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19: 57-69.
    • (2009) Genome Res , vol.19 , pp. 57-69
    • Ben Amor, B.1    Wirth, S.2    Merchan, F.3    Laporte, P.4    D'Aubenton-Carafa, Y.5
  • 13
    • 58149375464 scopus 로고    scopus 로고
    • Small regulatory non-coding RNAs in bacteria: Physiology and mechanistic aspects
    • Repoila F, Darfeuille F (2009) Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biol Cell 101: 117-131.
    • (2009) Biol Cell , vol.101 , pp. 117-131
    • Repoila, F.1    Darfeuille, F.2
  • 16
    • 81755162780 scopus 로고    scopus 로고
    • Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA
    • Sharwood RE, Halpert M, Luro S, Schuster G, Stern DB (2011) Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA. RNA 17: 2165-2176.
    • (2011) RNA , vol.17 , pp. 2165-2176
    • Sharwood, R.E.1    Halpert, M.2    Luro, S.3    Schuster, G.4    Stern, D.B.5
  • 17
    • 14844365722 scopus 로고    scopus 로고
    • Expression of complementary RNA from chloroplast transgenes affects editing efficiency of transgene and endogenous chloroplast transcripts
    • DOI 10.1093/nar/gki286
    • Hegeman CE, Halter CP, Owens TG, Hanson MR (2005) Expression of complementary RNA from chloroplast transgenes affects editing efficiency of transgene and endogenous chloroplast transcripts. Nucleic Acids Res 33: 1454-1464. (Pubitemid 41418375)
    • (2005) Nucleic Acids Research , vol.33 , Issue.5 , pp. 1454-1464
    • Hegeman, C.E.1    Halter, C.P.2    Owens, T.G.3    Hanson, M.R.4
  • 18
    • 77957151610 scopus 로고    scopus 로고
    • Overexpression of a natural chloroplast-encoded antisense RNA in tobacco destabilizes 5S rRNA and retards plant growth
    • Hotto AM, Huston ZE, Stern DB (2010) Overexpression of a natural chloroplast-encoded antisense RNA in tobacco destabilizes 5S rRNA and retards plant growth. BMC Plant Biol 10: 213.
    • (2010) BMC Plant Biol , vol.10 , pp. 213
    • Hotto, A.M.1    Huston, Z.E.2    Stern, D.B.3
  • 20
    • 84857877933 scopus 로고    scopus 로고
    • Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
    • Clark TA, Murray IA, Morgan RD, Kislyuk AO, Spittle KE, et al. (2012) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res 40: e29.
    • (2012) Nucleic Acids Res , vol.40
    • Clark, T.A.1    Murray, I.A.2    Morgan, R.D.3    Kislyuk, A.O.4    Spittle, K.E.5
  • 21
    • 0035839055 scopus 로고    scopus 로고
    • DNA methylation and epigenetic inheritance in plants and filamentous fungi
    • DOI 10.1126/science.293.5532.1070
    • Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293: 1070-1074. (Pubitemid 32758076)
    • (2001) Science , vol.293 , Issue.5532 , pp. 1070-1074
    • Martienssen, R.A.1    Colot, V.2
  • 22
    • 34249330696 scopus 로고    scopus 로고
    • Epigenetic inheritance in plants
    • DOI 10.1038/nature05917, PII NATURE05917
    • Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447: 418-424. (Pubitemid 46816748)
    • (2007) Nature , vol.447 , Issue.7143 , pp. 418-424
    • Henderson, I.R.1    Jacobsen, S.E.2
  • 24
    • 77952967431 scopus 로고    scopus 로고
    • Direct detection of DNA methylation during single-molecule, real-time sequencing
    • Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, et al. (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 7: 461-465.
    • (2010) Nat Methods , vol.7 , pp. 461-465
    • Flusberg, B.A.1    Webster, D.R.2    Lee, J.H.3    Travers, K.J.4    Olivares, E.C.5
  • 25
    • 84862293682 scopus 로고    scopus 로고
    • A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods
    • Sultan M, Dokel S, Amstislavskiy V, Wuttig D, Sultmann H, et al. (2012) A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods. Biochem Biophys Res Commun 422: 643-646.
    • (2012) Biochem Biophys Res Commun , vol.422 , pp. 643-646
    • Sultan, M.1    Dokel, S.2    Amstislavskiy, V.3    Wuttig, D.4    Sultmann, H.5
  • 26
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7: 562-578.
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5
  • 27
    • 77949512406 scopus 로고    scopus 로고
    • Tablet-next generation sequence assembly visualization
    • Milne I, Bayer M, Cardle L, Shaw P, Stephen G, et al. (2010) Tablet-next generation sequence assembly visualization. Bioinformatics 26: 401-402.
    • (2010) Bioinformatics , vol.26 , pp. 401-402
    • Milne, I.1    Bayer, M.2    Cardle, L.3    Shaw, P.4    Stephen, G.5
  • 28
    • 79952189030 scopus 로고    scopus 로고
    • Strandspecific real-time RT-PCR for distinguishing influenza vRNA, cRNA, and mRNA
    • Kawakami E, Watanabe T, Fujii K, Goto H, Watanabe S, et al. (2011) Strandspecific real-time RT-PCR for distinguishing influenza vRNA, cRNA, and mRNA. J Virol Methods 173: 1-6.
    • (2011) J Virol Methods , vol.173 , pp. 1-6
    • Kawakami, E.1    Watanabe, T.2    Fujii, K.3    Goto, H.4    Watanabe, S.5
  • 29
    • 0035710746 scopus 로고    scopus 로고
    • -DeltaDeltaCT method
    • DOI 10.1006/meth.2001.1262
    • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408. (Pubitemid 34164012)
    • (2001) Methods , vol.25 , Issue.4 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2
  • 30
    • 33845624887 scopus 로고    scopus 로고
    • Microarray validation: Factors influencing correlation between oligonucleotide microarrays and real-time PCR
    • DOI 10.1251/bpo126
    • Morey JS, Ryan JC, Van Dolah FM (2006) Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR. Biol Proced Online 8: 175-193. (Pubitemid 44942143)
    • (2006) Biological Procedures Online , vol.8 , Issue.1 , pp. 175-193
    • Morey, J.S.1    Ryan, J.C.2    Van Dolah, F.M.3
  • 32
    • 0030774006 scopus 로고    scopus 로고
    • Transcription and translation in chloroplasts
    • DOI 10.1016/S1360-1385(97)01088-1
    • Stern DS, Higgs DC, Yang J (1997) Transcription and translation in chloroplasts. Trends in plant science 2: 308-315. (Pubitemid 27369348)
    • (1997) Trends in Plant Science , vol.2 , Issue.8 , pp. 308-315
    • Stern, D.B.1    Higgs, D.C.2    Yang, J.3
  • 33
    • 77958527485 scopus 로고    scopus 로고
    • The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.)
    • Yang M, Zhang X, Liu G, Yin Y, Chen K, et al. (2010) The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5: e12762.
    • (2010) PLoS One , vol.5
    • Yang, M.1    Zhang, X.2    Liu, G.3    Yin, Y.4    Chen, K.5
  • 34
    • 18144428771 scopus 로고    scopus 로고
    • Breakthrough in chloroplast genetic engineering of agronomically important crops
    • DOI 10.1016/j.tibtech.2005.03.008
    • Daniell H, Kumar S, Dufourmantel N (2005) Breakthrough in chloroplast genetic engineering of agronomically important crops. Trends Biotechnol 23: 238-245. (Pubitemid 40615536)
    • (2005) Trends in Biotechnology , vol.23 , Issue.5 , pp. 238-245
    • Daniell, H.1    Kumar, S.2    Dufourmantel, N.3
  • 35
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 36
    • 80052960863 scopus 로고    scopus 로고
    • Next-generation transcriptome assembly
    • Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682.
    • (2011) Nat Rev Genet , vol.12 , pp. 671-682
    • Martin, J.A.1    Wang, Z.2
  • 37
    • 69249217649 scopus 로고    scopus 로고
    • Regulatory roles of natural antisense transcripts
    • Faghihi MA, Wahlestedt C (2009) Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 10: 637-643.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 637-643
    • Faghihi, M.A.1    Wahlestedt, C.2
  • 38
    • 68849101462 scopus 로고    scopus 로고
    • Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues
    • Grigoriadis A, Oliver GR, Tanney A, Kendrick H, Smalley MJ, et al. (2009) Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues. BMC Genomics 10: 324.
    • (2009) BMC Genomics , vol.10 , pp. 324
    • Grigoriadis, A.1    Oliver, G.R.2    Tanney, A.3    Kendrick, H.4    Smalley, M.J.5
  • 39
    • 84876320555 scopus 로고    scopus 로고
    • Conserved expression of natural antisense transcripts in mammals
    • Ling MH, Ban Y, Wen H, Wang SM, Ge SX (2013) Conserved expression of natural antisense transcripts in mammals. BMC Genomics 14: 243.
    • (2013) BMC Genomics , vol.14 , pp. 243
    • Ling, M.H.1    Ban, Y.2    Wen, H.3    Wang, S.M.4    Ge, S.X.5
  • 40
    • 33845880624 scopus 로고    scopus 로고
    • Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    • DOI 10.1038/ng1929, PII NG1929
    • Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genomewide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: 61-69. (Pubitemid 46026502)
    • (2007) Nature Genetics , vol.39 , Issue.1 , pp. 61-69
    • Zilberman, D.1    Gehring, M.2    Tran, R.K.3    Ballinger, T.4    Henikoff, S.5
  • 41
    • 34250188803 scopus 로고    scopus 로고
    • Genomic patterns of DNA methylation: Targets and function of an epigenetic mark
    • DOI 10.1016/j.ceb.2007.04.011, PII S0955067407000634, Nucleus and Gene Expression
    • Weber M, Schubeler D (2007) Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr Opin Cell Biol 19: 273-280. (Pubitemid 46899512)
    • (2007) Current Opinion in Cell Biology , vol.19 , Issue.3 , pp. 273-280
    • Weber, M.1    Schubeler, D.2
  • 42
    • 75549089556 scopus 로고    scopus 로고
    • Genomewide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer
    • Cheung HH, Lee TL, Davis AJ, Taft DH, Rennert OM, et al. (2010) Genomewide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer. Br J Cancer 102: 419-427.
    • (2010) Br J Cancer , vol.102 , pp. 419-427
    • Cheung, H.H.1    Lee, T.L.2    Davis, A.J.3    Taft, D.H.4    Rennert, O.M.5
  • 43
    • 84863115947 scopus 로고    scopus 로고
    • A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice
    • Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, et al. (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci U S A 109: 2654-2659.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 2654-2659
    • Ding, J.1    Lu, Q.2    Ouyang, Y.3    Mao, H.4    Zhang, P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.