A Two-Edged Role for the Transposable Element Kiddo in the rice ubiquitin2 Promoterw⃞

Miniature inverted repeat transposable elements (MITEs) are thought to be a driving force for genome evolution. Although numerous MITEs are found associated with genes, little is known about their function in gene regulation. Whereas the rice ubiquitin2 (rubq2) promoter in rice (Oryza sativa) line IR24 contains two nested MITEs (Kiddo and MDM1), that in line T309 has lost Kiddo, providing an opportunity to understand the role of MITEs in promoter function. No difference in endogenous rubq2 transcript levels between T309 and IR24 was evident using RT-PCR. However, promoter analysis using both transient and stably transformed calli revealed that Kiddo contributed some 20% of the total expression. Bisulfite genomic sequencing of the rubq2 promoters revealed specific DNA methylation at both symmetric and asymmetric cytosine residues on the MITE sequences, possibly induced by low levels of homologous transcripts. When methylation of the MITEs was blocked by 5-azacytidine treatment, a threefold increase in the endogenous rubq2 transcript level was detected in IR24 compared with that in T309. Together with the observed MITE methylation pattern, the detection of low levels of transcripts, but not small RNAs, corresponding to Kiddo and MDM1 suggested that RNA-dependent DNA methylation is induced by MITE transcripts. We conclude that, although Kiddo enhances transcription from the rubq2 promoter, this effect is mitigated by sequence-specific epigenetic modification.

[1]  Cédric Feschotte,et al.  Miniature Inverted-Repeat Transposable Elements and Their Relationship to Established DNA Transposons , 2002 .

[2]  A. Smit,et al.  Tiggers and DNA transposon fossils in the human genome. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Sean R. Eddy,et al.  An active DNA transposon family in rice , 2003, Nature.

[4]  J. Casacuberta,et al.  Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. , 2003, Gene.

[5]  M. Matzke,et al.  Homology-dependent gene silencing and host defense in plants. , 2002, Advances in genetics.

[6]  C. Feschotte,et al.  Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. , 2000, Molecular biology and evolution.

[7]  N. Fedoroff,et al.  Epigenetic regulation of the maize Spm transposable element: Novel activation of a methylated promoter by TnpA , 1994, Cell.

[8]  Guojun Yang,et al.  MAK, a computational tool kit for automated MITE analysis , 2003, Nucleic Acids Res..

[9]  N Okada,et al.  SINE insertions: powerful tools for molecular systematics. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[10]  J. Schiefelbein,et al.  RNA splicing permits expression of a maize gene with a defective Suppressor-mutator transposable element insertion in an exon. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[11]  H. Robertson.  Members of the pogo superfamily of DNA-mediated transposons in the human genome , 1996, Molecular and General Genetics MGG.

[12]  Gangning Liang,et al.  Cooperativity between DNA Methyltransferases in the Maintenance Methylation of Repetitive Elements , 2002, Molecular and Cellular Biology.

[13]  S. Lowe,et al.  Genes and transposons are differentially methylated in plants, but not in mammals. , 2003, Genome research.

[14]  Marjori Matzke,et al.  Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation , 2003, Current Biology.

[15]  Zhanjiang Liu,et al.  Effects of Insert Size on Transposition Efficiency of the Sleeping Beauty Transposon in Mouse Cells , 2001, Marine Biotechnology.

[16]  Jiang,et al.  Structure, expression and promoter activity of two polyubiquitin genes from rice (Oryza sativa L.). , 2000, Plant science : an international journal of experimental plant biology.

[17]  M. Matzke,et al.  HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double‐stranded RNA , 2002, The EMBO journal.

[18]  S. Wessler,et al.  P instability factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[19]  S. Wessler,et al.  Tourist: a large family of small inverted repeat elements frequently associated with maize genes. , 1992, The Plant cell.

[20]  D. Dorsett.  Potentiation of a polyadenylylation site by a downstream protein-DNA interaction. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[21]  R. Plasterk,et al.  Sleeping Beauty, a wide host-range transposon vector for genetic transformation in vertebrates. , 2000, Journal of molecular biology.

[22]  S. Wessler,et al.  LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. , 1995, Current opinion in genetics & development.

[23]  H. Biessmann,et al.  Frequent transpositions of Drosophila melanogaster HeT‐A transposable elements to receding chromosome ends. , 1992, The EMBO journal.

[24]  S. Wessler,et al.  The maize transposable element Ds is spliced from RNA. , 1987, Science.

[25]  N. Fedoroff,et al.  Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable element. , 1988, Genes & development.

[26]  N. Fedoroff.  The heritable activation of cryptic Suppressor-mutator elements by an active element. , 1989, Genetics.

[27]  P. Dimitri,et al.  Revising the selfish DNA hypothesis: new evidence on accumulation of transposable elements in heterochromatin. , 1999, Trends in genetics : TIG.

[28]  T. Bureau,et al.  Tc8, a Tourist-like transposon in Caenorhabditis elegans. , 2001, Genetics.

[29]  S. Wessler,et al.  Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. , 1994, The Plant cell.

[30]  Z. Tu,et al.  Three novel families of miniature inverted-repeat transposable elements are associated with genes of the yellow fever mosquito, Aedes aegypti. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[31]  J. Paszkowski,et al.  Gene silencing and DNA methylation processes. , 2001, Current opinion in plant biology.

[32]  T. Hall,et al.  Epigenetic Transcriptional Silencing and 5-Azacytidine-Mediated Reactivation of a Complex Transgene in Rice , 1997, Plant physiology.

[33]  J. Jeddeloh,et al.  Arabidopsis MET1 cytosine methyltransferase mutants. , 2003, Genetics.

[34]  V. Corces,et al.  DNA position-specific repression of transcription by a Drosophila zinc finger protein. , 1992, Genes & development.

[35]  N. Fedoroff,et al.  Patterns of developmental and heritable change in methylation of the Suppressor-mutator transposable element , 1989 .

[36]  R. Levis,et al.  HeT-A, a transposable element specifically involved in "healing" broken chromosome ends in Drosophila melanogaster , 1992, Molecular and cellular biology.

[37]  Guojun Yang,et al.  MDM-1 and MDM-2: Two Mutator-Derived MITE Families in Rice , 2003, Journal of Molecular Evolution.

[38]  H. Saedler,et al.  Molecular interactions between the components of the En‐I transposable element system of Zea mays , 1985, The EMBO journal.

[39]  P. Jeffrey,et al.  Regulation of Heterochromatic Silencing and Histone H 3 Lysine-9 Methylation by RNAi , 2002 .

[40]  T. Hall,et al.  Longevity of 5-azacytidine-mediated gene expression and re-establishment of silencing in transgenic rice , 1998, Plant Molecular Biology.

[41]  B. Mcclintock.  The Suppressor-Mutator System of Control of Gene Action in Maize , 1958 .

[42]  Ira M. Hall,et al.  Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi , 2002, Science.

[43]  T. Bureau,et al.  Survey of transposable elements from rice genomic sequences. , 2008, The Plant journal : for cell and molecular biology.

[44]  Marjori Matzke,et al.  Genetic analysis of RNA-mediated transcriptional gene silencing. , 2004, Biochimica et biophysica acta.

[45]  S. Wessler,et al.  Excision of Ds produces waxy proteins with a range of enzymatic activities. , 1986, The EMBO journal.

[46]  D. Dorsett,et al.  Expression of the cut locus in the Drosophila wing margin is required for cell type specification and is regulated by a distant enhancer. , 1991, Development.

[47]  J. Bennetzen,et al.  Transposable element contributions to plant gene and genome evolution , 2004, Plant Molecular Biology.

[48]  E. Coen,et al.  Complementary floral homeotic phenotypes result from opposite orientations of a transposon at the plena locus of antirrhinum , 1993, Cell.

[49]  B. Reinhart,et al.  MicroRNAs in plants. , 2002, Genes & development.

[50]  Yutaka Okumoto,et al.  Mobilization of a transposon in the rice genome , 2003, Nature.

[51]  J. P. Jackson,et al.  Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation , 2001, Science.

[52]  E. Finnegan,et al.  Plant DNA methyltransferases , 2000, Plant Molecular Biology.

[53]  N.-S. Kim,et al.  Genetic variations of AA genome Oryza species measured by MITE-AFLP , 2003, Theoretical and Applied Genetics.

[54]  A. Barkan,et al.  Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[55]  T. Hall,et al.  Kiddo, a new transposable element family closely associated with rice genes , 2001, Molecular Genetics and Genomics.

[56]  Jeremy D. Edwards,et al.  Sources and predictors of resolvable indel polymorphism assessed using rice as a model , 2004, Molecular Genetics and Genomics.

[57]  S. Hake,et al.  Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations. , 1994, Genetics.

[58]  N. Fedoroff,et al.  TnpA trans-activates methylated maize Suppressor-mutator transposable elements in transgenic tobacco. , 1993, Genetics.

[59]  W. Belknap,et al.  Characterization of Repetitive DNA Elements in Arabidopsis , 1999, Journal of Molecular Evolution.

[60]  M. Matzke,et al.  Transcriptional silencing and promoter methylation triggered by double‐stranded RNA , 2000, The EMBO journal.

[61]  S. Jacobsen,et al.  Role of the Arabidopsis DRM Methyltransferases in De Novo DNA Methylation and Gene Silencing , 2002, Current Biology.

[62]  Kazuhiro Kikuchi,et al.  The plant MITE mPing is mobilized in anther culture , 2003, Nature.

[63]  T. Schmidt.  LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes , 1999, Plant Molecular Biology.

[64]  S. Wessler,et al.  Miniature inverted repeat transposable elements help create genomic diversity in maize and rice. , 2001 .

[65]  S. Wessler,et al.  Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[66]  J. Haseloff,et al.  GFP in plants. , 1995, Trends in genetics : TIG.

[67]  M. Cervera,et al.  The use of FISH in chromosomal localization of transgenes in rice. , 2001, Methods in cell science : an official journal of the Society for In Vitro Biology.

[68]  A. Wolffe,et al.  Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon beta-phaseolin gene activation. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[69]  N. Fedoroff,et al.  Epigenetic regulation of the maize Spm transposable element: novel activation of a methylated promoter by TnpA. , 1994, Cell.

[70]  V. Corces,et al.  Retrotransposon‐induced overexpression of a homeobox gene causes defects in eye morphogenesis in Drosophila. , 1991, The EMBO journal.

[71]  O. Mathieu,et al.  RNA-directed DNA methylation , 2004, Journal of Cell Science.

[72]  M. Carmell,et al.  Posttranscriptional Gene Silencing in Plants , 2006 .

[73]  D. Dorsett,et al.  Repression of hsp70 heat shock gene transcription by the suppressor of hairy-wing protein of Drosophila melanogaster , 1991, Molecular and cellular biology.

[74]  M. Davisson,et al.  Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. , 1994, Genes & development.

[75]  C. Chu,et al.  ESTABLISHMENT OF AN EFFICIENT MEDIUM FOR ANTHER CULTURE OF RICE THROUGH COMPARATIVE EXPERIMENTS ON THE NITROGEN SOURCES , 1975 .

[76]  H. Uchimiya,et al.  Transformation in Rice , 1991 .

[77]  T. Komari,et al.  Transformation of rice mediated by Agrobacterium tumefaciens , 1997, Plant Molecular Biology.

[78]  C. Hutchison,et al.  Ty1 sequence with enhancer and mating-type-dependent regulatory activities , 1987, Molecular and cellular biology.

[79]  M. Matzke,et al.  RNA-directed DNA methylation in Arabidopsis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[80]  S. Melquist,et al.  Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis. , 2003, Genes & development.

[81]  A. Monfort,et al.  Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana: characterisation of the Emigrant family of elements. , 1998, The Plant journal : for cell and molecular biology.

[82]  T. Komari,et al.  Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. , 1994, The Plant journal : for cell and molecular biology.