Antisense transcripts with rice full-length cDNAs
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Vanhee-Brossollet C, Vaquero C: Do natural antisense transcripts make sense in eukaryotes?Gene 1998, 211:1–9.
Terryn N, Rouze P: The sense of naturally transcribed antisense RNAs in plants.Trends Plant Sci 2000, 5:394–396.
Moore T, Constancia M, Zubair M, Bailleul B, Feil R, Sasaki H, Reik W: Multiple imprinted sense and antisense transcripts, differential methylation and tandem repeats in a putative imprinting control region upstream of mouse Igf2.Proc Natl Acad Sci USA 1997, 94:12509–12514.
Sleutels F, Zwart R, Barlow DP: The non-coding Air RNA is required for silencing autosomal imprinted genes.Nature 2002, 415:810–813.
Yamasaki K, Joh K, Ohta T, Masuzaki H, Ishimaru T, Mukai T, Niikawa N, Ogawa M, Wagstaff J, Kishino T: Neurons but not glial cells show reciprocal imprinting of sense and antisense transcripts ofUbe3a.Hum Mol Genet 2003, 12:837–847.
Tufarelli C, Stanley JA, Garrick D, Sharpe JA, Ayyub H, Wood WG, Higgs DR: Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease.Nat Genet 2003, 34:157–165.
Lee JT, Davidow LS, Warshawsky D: Tsix, a gene antisense toXistat the X-inactivation centre.Nat Genet 1999, 21:400–404.
Willard HF, Carrel L: Making sense (and antisense) of the X inactivation center.Proc Natl Acad Sci USA 2001, 98:10025–10027.
Migeon BR, Chowdhury AK, Dunston JA, McIntosh I: Identification ofTSIX, encoding an RNA antisense to humanXIST, reveals differences from its murine counterpart: implications for X inactivation.Am J Hum Genet 2001, 69:951–960.
Munroe SH, Lazar MA: Inhibition ofc-erbAmRNA splicing by a naturally occurring antisense RNA.J Biol Chem 1991, 266:22083–22086.
Sureau A, Soret J, Guyon C, Gaillard C, Dumon S, Keller M, Crisanti P, Perbal B: Characterization of multiple alternative RNAs resulting from antisense transcription of the PR264/SC35 splicing factor gene.Nucleic Acids Res 1997, 25:4513–4522.
Peters NT, Rohrbach JA, Zalewski BA, Byrkett CM, Vaughn JC: RNA editing and regulation ofDrosophila4f-rnp expression by sas-10 antisense readthrough mRNA transcripts.RNA 2003, 9:698–710.
Billy E, Brondani V, Zhang H, Muller U, Filipowicz W: Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines.Proc Natl Acad Sci USA 2001, 98:14428–14433.
Anderson S, Bankier AT, Barrell BG, Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al.: Sequence and organization of the human mitochondrial genome.Nature 1981, 290:457–465.
Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA: Sequence and organization of the mouse mitochondrial DNA.Cell 1981, 26:167–180.
Spencer CA, Gietz RD, Hodgetts RB: Overlapping transcription units in the dopa decarboxylase region ofDrosophila.Nature 1986, 322:279–281.
Lehner B, Williams G, Campbell RD, Sanderson CM: Antisense transcripts in the human genome.Trends Genet 2002, 18:63–65.
Shendure J, Church GM: Computational discovery of sense-antisense transcription in the human and mouse genomes.Genome Biol 2002, 3:research0044.1–0044.14.
Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, et al.: Widespread occurrence of antisense transcription in the human genome.Nat Biotechnol 2003, 21:379–386.
Kiyosawa H, Yamanaka I, Osato N, Kondo S, RIKEN GER Group and GSL Members, Hayashizaki Y: Antisense-transcripts with FANTOM2 clone set and their implications for gene regulation.Genome Res 2003, 13:1324–1334.
Plant ncRNA database[http://www.prl.msu.edu/PLANTncRNAs/database.html]
Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, et al.: Empirical analysis of transcriptional activity in theArabidopsisgenome.Science 2003, 302:842–846.
Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, et al.: Collection, mapping, and annotation of 28,000 full-length cDNA clones fromJaponicarice.Science 2003, 301:376–379.
Osato N, Itoh M, Konno H, Kondo S, Shibata K, Carninci P, Shiraki T, Shinagawa A, Arakawa T, Kikuchi S, et al.: A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs.Genome Res 2002, 12:1127–1134.
Pearson WR, Lipman DJ: Improved tools for biological sequence comparison.Proc Natl Acad Sci USA 1988, 85:2444–2448.
Supplementary materials for this study[http://cdna01.dna.affrc.go.jp/cDNA/Analysis/antisenseweb]
Walker DR, Koonin EV: SEALS: a system for easy analysis of lots of sequences.Proc Int Conf Intell Syst Mol Biol 1997, 5:333–339.
Shimatani Z, Yazaki J, Kishimoto N, Hashimoto A, Nagata Y, Shimbo K, Fujii F, Taya T, Tonouchi M, Nelson C., et al.: 22,000 single strand oligo-based microarray system for expression analysis of rice genes.Seventh International Congress of Plant Molecular Biology 2003. Abstract
Carter MG, Hamatani T, Sharov AA, Carmack CE, Qian Y, Aiba K, Ko NT, Dudekula DB, Brzoska PM, Hwang SS, et al.: In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling.Genome Res 2003, 13:1011–1021.
Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, et al.: Sequence and analysis of rice chromosome 4.Nature 2002, 420:316–320.
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al.: A draft sequence of the rice genome (Oryza sativaL. ssp.japonica).Science 2002, 296:92–100.
Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, et al.: The genome sequence and structure of rice chromosome 1.Nature 2002, 420:312–316.
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al.: A draft sequence of the rice genome (Oryza sativaL. ssp. indica).Science 2002, 296:79–92.
FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.Nature 2002, 420:563–573.
Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, et al.: Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.Genome Res 2003, 13:1273–1289.
Furuno M, Kasukawa T, Saito R, Adachi J, Suzuki H, Baldarelli R, Hayashizaki Y, Okazaki Y: CDS annotation in full-length cDNA sequence.Genome Res 2003, 13:1478–1487.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, et al.: The InterPro Database, 2003 brings increased coverage and new features.Nucleic Acids Res 2003, 31:315–318.
Que Q, Wang HY, Jorgensen RA: Distinct patterns of pigment suppression are produced by allelic sense and antisense chalcone synthase transgenes in petunia flowers.Plant J 1998, 13:401–409.
Jorgensen RA, Que Q, Stam M: Do unintended antisense transcripts contribute to sense cosuppression in plants?Trends Genet 1999, 15:11–12.
Hamilton AJ, Baulcombe DC: A species of small antisense RNA in posttranscriptional gene silencing in plants.Science 1999, 286:950–952.
Vaucheret H, Beclin C, Fagard M: Post-transcriptional gene silencing in plants.J Cell Sci 2001, 114:3083–3091.
Wang MB, Waterhouse PM: Application of gene silencing in plants.Curr Opin Plant Biol 2002, 5:146–150.
Tang G, Reinhart BJ, Bartel DP, Zamore PD: A biochemical framework for RNA silencing in plants.Genes Dev 2003, 17:49–63.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool.J Mol Biol 1990, 215:403–410.
Wheelan SJ, Church DM, Ostell JM: Spidey: a tool for mRNA-to-genomic alignments.Genome Res 2001, 11:1952–1957.