Organization, not duplication, triggers silencing in a complex transgene locus in rice View Full Text


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Article Info

DATE

2005-06

AUTHORS

Guojun Yang, Yeon-Hee Lee, Yiming Jiang, Siva P. Kumpatla, Timothy C. Hall

ABSTRACT

Despite the presence in nature of many functional gene families that contain several to many highly similar sequences, the presence of identical DNA sequence repeats is widely thought to predispose transgene inserts to homology dependent gene silencing (HDGS). The induction of transcriptional gene silencing (TGS) by RNAs homologous to promoter sequences has been reported recently in Arabidopsis and humans. However, mechanisms for TGS have not been studied in detail for rice, the most widely cultivated crop plant. Taking advantage of a well-characterized homozygous silenced transgenic rice line (siJKA), supertransformation was performed with a binary vector bearing mUbi1 and 35S promoter sequences identical to those in the resident transgenes. Analysis of the incoming and resident transgenes in the supertransformants revealed that the incoming mUbi1 transgene promoter was not silenced whereas the incoming 35S transgene promoter was silenced. That the resident silenced mUbi1-bar was not reactivated in these experiments as a result of passage through tissue culture and regeneration was established by the finding that regenerants from siJKA immature embryos were all silenced for mUbi1-bar. In a parallel experiment, when wild type rice calli were transformed with the same binary vector, neither of the incoming transgene promoters was silenced. Following 5-azacytidine (5-azaC) treatment of siJKA, aberrant RNA species corresponding to the 35S promoter, but not to the mUbi1 promoter, were detected. Nevertheless, no 21–25 nt RNAs corresponding to the 35S promoter sequence were detected. These results, together with detailed analyses of the progenies from the primary transformants and supertransformants, revealed that HDGS of the resident silenced locus was caused not by simple transgene duplication, but by aberrant transcripts derived from rearranged promoters present in siJKA. Practical consequences of this study include a justification for the use of multiple copies of a given promoter for transformation without inducing silencing, provided that their genomic integration does not result in aberrant transcription of the promoters. More... »

PAGES

351-366

References to SciGraph publications

  • 1998-02. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans in NATURE
  • 2001-03. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins in NATURE
  • 1996-04. Creation of genomic methylation patterns in NATURE GENETICS
  • 1995-01. Molecular and genetic characterization of elite transgenic rice plants produced by electric-discharge particle acceleration in THEORETICAL AND APPLIED GENETICS
  • 1994-09. Structure and function of selectable and non-selectable transgenes in maize after introduction by particle bombardment in PLANT MOLECULAR BIOLOGY
  • 1993-09. Epigenetic repeat-induced gene silencing (RIGS) inArabidopsis in PLANT MOLECULAR BIOLOGY
  • 2000-06. Transgene silencing in monocots in PLANT MOLECULAR BIOLOGY
  • 1990-06. Identificaton and characterization of stamen- and tapetum-specific genes from tomato in MOLECULAR GENETICS AND GENOMICS
  • 1998-12. Longevity of 5-azacytidine-mediated gene expression and re-establishment of silencing in transgenic rice in PLANT MOLECULAR BIOLOGY
  • 2001-02. Post-transcriptional gene silencing by double-stranded RNA in NATURE REVIEWS GENETICS
  • 2002-03-17. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase in NATURE
  • 1994-03. Gene inactivation triggered by recognition between DNA repeats in CELLULAR AND MOLECULAR LIFE SCIENCES
  • 2001-09. Characterization of rice transformed via an Agrobacterium-mediated inflorescence approach in MOLECULAR BREEDING
  • 2003-08-20. Control of leaf morphogenesis by microRNAs in NATURE
  • 2001-01. Role for a bidentate ribonuclease in the initiation step of RNA interference in NATURE
  • 1994-07. Inheritance and expression of a transgene insert in an aneuploid tobacco line in MOLECULAR GENETICS AND GENOMICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s11103-005-5101-y

    DOI

    http://dx.doi.org/10.1007/s11103-005-5101-y

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1007396070

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/16021400


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    37 schema:description Despite the presence in nature of many functional gene families that contain several to many highly similar sequences, the presence of identical DNA sequence repeats is widely thought to predispose transgene inserts to homology dependent gene silencing (HDGS). The induction of transcriptional gene silencing (TGS) by RNAs homologous to promoter sequences has been reported recently in Arabidopsis and humans. However, mechanisms for TGS have not been studied in detail for rice, the most widely cultivated crop plant. Taking advantage of a well-characterized homozygous silenced transgenic rice line (siJKA), supertransformation was performed with a binary vector bearing mUbi1 and 35S promoter sequences identical to those in the resident transgenes. Analysis of the incoming and resident transgenes in the supertransformants revealed that the incoming mUbi1 transgene promoter was not silenced whereas the incoming 35S transgene promoter was silenced. That the resident silenced mUbi1-bar was not reactivated in these experiments as a result of passage through tissue culture and regeneration was established by the finding that regenerants from siJKA immature embryos were all silenced for mUbi1-bar. In a parallel experiment, when wild type rice calli were transformed with the same binary vector, neither of the incoming transgene promoters was silenced. Following 5-azacytidine (5-azaC) treatment of siJKA, aberrant RNA species corresponding to the 35S promoter, but not to the mUbi1 promoter, were detected. Nevertheless, no 21–25 nt RNAs corresponding to the 35S promoter sequence were detected. These results, together with detailed analyses of the progenies from the primary transformants and supertransformants, revealed that HDGS of the resident silenced locus was caused not by simple transgene duplication, but by aberrant transcripts derived from rearranged promoters present in siJKA. Practical consequences of this study include a justification for the use of multiple copies of a given promoter for transformation without inducing silencing, provided that their genomic integration does not result in aberrant transcription of the promoters.
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