Low abundant spacer 5S rRNA transcripts are frequently polyadenylated in Nicotiana (original) (raw)
Ali HB, Fransz P, Schubert I (2000) Localization of 5S RNA genes on tobacco chromosomes. Chromosome Res 8:85–87 ArticlePubMedCAS Google Scholar
Barciszewska MZ (1994) Interaction of higher plant ribosomal 5S RNAs with Xenopus laevis transcriptional factor IIIA. Acta Biochim Pol 41:17–24 PubMedCAS Google Scholar
Buhler M, Haas W, Gygi SP, Moazed D (2007) RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 129:707–721 ArticlePubMedCAS Google Scholar
Chekanova JA, Dutko JA, Mian IS, Belostotsky DA (2002) Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3′→5’ exonuclease containing S1 and KH RNA-binding domains. Nucleic Acids Res 30:695–700 ArticlePubMedCAS Google Scholar
Cloix C, Tutois S, Mathieu O, Cuvillier C, Espagnol MC, Picard G, Tourmente S (2000) Analysis of 5S rDNA arrays in Arabidopsis thaliana: physical mapping and chromosome-specific polymorphisms. Genome Res 10:679–690 ArticlePubMedCAS Google Scholar
Cloix C, Tutois S, Yukawa Y, Mathieu O, Cuvillier C, Espagnol MC, Picard G, Tourmente S (2002) Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNA. Genome Res 12:132–144 ArticlePubMedCAS Google Scholar
Cronn RC, Zhao X, Paterson AH, Wendel JF (1996) Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J Mol Evol 42:685–705 ArticlePubMedCAS Google Scholar
Dadejova M, Lim Y, Souckova-Skalicka K, Matyasek R, Leitch AR, Grandbastien M-A, Kovarik A (2007) Transcription activity of rRNA genes correlates with a tendency towards intergenomic homogenization in Nicotiana allotetraploids. New Phytol 166:291–303 Google Scholar
Fojtova M, Bleys A, Bedrichova J, Van Houdt H, Krizova K, Depicker A, Kovarik A (2006) The trans-silencing capacity of invertedly repeated transgenes depends on their epigenetic state in tobacco. Nucleic Acids Res 34:2280–2293 ArticlePubMedCAS Google Scholar
Fulnecek J, Lim KY, Leitch AR, Kovarik A, Matyasek R (2002a) Evolution and structure of 5S rDNA loci in allotetraploid Nicotiana tabacum and its putative parental species. Heredity 88:19–25 ArticlePubMedCAS Google Scholar
Fulnecek J, Matyasek R, Kovarik A (2002b) Distribution of 5-methylcytosine residues in 5S rRNA genes in Arabidopsis thaliana and Secale cereale. Mol Genet Genomics 268:510–517 ArticlePubMedCAS Google Scholar
Fulnecek J, Matyasek R, Kovarik A (2006) Plant 5S rDNA has multiple alternative nucleosome positions. Genome 49:840–850 ArticlePubMedCAS Google Scholar
Fulnecek J, Matyasek R, Kovarik A, Bezdek M (1998) Mapping of 5-methylcytosine residues in Nicotiana tabacum 5S rRNA genes by genomic sequencing. Mol Gen Genet 259:133–141 ArticlePubMedCAS Google Scholar
Grierson D, Hemleben V (1977) Ribonucleic acid from the higher plant Matthiola incana. Molecular weight measurements and DNA-RNA hybridisation studies. Biochim Biophys Acta 475:424–436 PubMedCAS Google Scholar
Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286:950–952 ArticlePubMedCAS Google Scholar
Hemleben V, Werts D (1988) Sequence organization and putative regulatory elements in the 5S rRNA genes of two higher plants (Vigna radiata and Matthiola incana). Gene 62:165–169 ArticlePubMedCAS Google Scholar
Kadaba S, Wang X, Anderson JT (2006) Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 12:508–521 ArticlePubMedCAS Google Scholar
Kellogg EA, Appels R (1995) Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Genetics 140:325–343 PubMedCAS Google Scholar
Lapitan NLV (1992) Organization and evolution of higher plant genomes. Genome 35:171–181 CAS Google Scholar
Lee Y, Melekhovets YF, Nazar RN (1995) Termination as factor in “quality control” during ribosome biogenesis. J Biol Chem 270:28003–28005 ArticlePubMedCAS Google Scholar
Lisitsky I, Klaff P, Schuster G (1996) Addition of destabilizing poly (A)-rich sequences to endonuclease cleavage sites during the degradation of chloroplast mRNA. Proc Natl Acad Sci USA 93:13398–13403 ArticlePubMedCAS Google Scholar
Mathieu O, Jasencakova Z, Vaillant I, Gendrel AV, Colot V, Schubert I, Tourmente S (2003a) Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis. Plant Cell 15:2929–2939 ArticlePubMedCAS Google Scholar
Mathieu O, Yukawa Y, Prieto JL, Vaillant I, Sugiura M, Tourmente S (2003b) Identification and characterization of transcription factor IIIA and ribosomal protein L5 from Arabidopsis thaliana. Nucleic Acids Res 31:2424–2433 ArticlePubMedCAS Google Scholar
Mathieu O, Yukawa Y, Sugiura M, Picard G, Tourmente S (2002) 5S rRNA genes expression is not inhibited by DNA methylation in Arabidopsis. Plant J 29:313–323 ArticlePubMedCAS Google Scholar
Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette MF, Matzke AJ (2004) Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta 1677:129–141 PubMedCAS Google Scholar
Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3’->5’ exoribonucleases. Cell 91:457–466 ArticlePubMedCAS Google Scholar
Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120:613–622 ArticlePubMedCAS Google Scholar
Platt T (1986) Transcription termination and the regulation of gene expression. Annu Rev Biochem 55:339–372 ArticlePubMedCAS Google Scholar
Proudfoot N (2004) New perspectives on connecting messenger RNA 3’ end formation to transcription. Curr Opin Cell Biol 16:272–278 ArticlePubMedCAS Google Scholar
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor Google Scholar
Schiebel K, von Waldburg G, Gerstner J, Hemleben V (1989) Termination of transcription of ribosomal RNA genes of mung bean occurs within a 175 bp repetitive element of the spacer region. Mol Gen Genet 218:302–307 ArticlePubMedCAS Google Scholar
Slomovic S, Laufer D, Geiger D, Schuster G (2006) Polyadenylation of ribosomal RNA in human cells. Nucleic Acids Res 34:2966–2975 ArticlePubMedCAS Google Scholar
Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J (2003) 5 S rRNA: structure and interactions. Biochem J 371:641–651 ArticlePubMedCAS Google Scholar
Theunissen O, Rudt F, Guddat U, Mentzel H, Pieler T (1992) RNA and DNA binding zinc fingers in Xenopus TFIIIA. Cell 13:679–690 Article Google Scholar
Vaillant I, Schubert I, Tourmente S, Mathieu O (2006) MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis. EMBO Rep 7:1273–1278 ArticlePubMedCAS Google Scholar
van Hoof A, Lennertz P, Parker R (2000) Yeast exosome mutants accumulate 3’-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol Cell Biol 20:441–452 ArticlePubMed Google Scholar
Venkateswarlu K, Lee SW, Nazar RN (1991) Conserved upstream sequence elements in plant 5S ribosomal RNA-encoding genes. Gene 105:249–254 ArticlePubMedCAS Google Scholar
Wahle E, Ruegsegger U (1999) 3’-End processing of pre-mRNA in eukaryotes. FEMS Microbiol Rev 23:277–295 PubMedCAS Google Scholar
Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:E104 ArticlePubMed Google Scholar
Yukawa Y, Sugita M, Choisne N, Small I, Sugiura M (2000) The TATA motif, the CAA motif and the poly(T) transcription termination motif are all important for transcription re-initiation on plant tRNA genes. Plant J 22:439–447 ArticlePubMedCAS Google Scholar
Zentgraf U, Ganal M, Hemleben V (1990) Length heterogeneity of the rRNA precursor in cucumber (Cucumis sativus). Plant Mol Biol 15:465–474 ArticlePubMedCAS Google Scholar