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Transposable Element Regulation in Rice and Arabidopsis: Diverse Patterns of Active Expression and siRNA-mediated Silencing

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Abstract

Transposable elements (TEs) are DNA segments that can mediate or cause movement within genomes. We performed a comprehensive, whole-genome analysis of annotated TEs in rice (Oryza sativa L.) and Arabidopsis thaliana, focusing on their expression (mRNA data) and silencing (small RNA data), and we compared these data with annotated genes that are not annotated as transposons. TEs demonstrated higher levels of antisense mRNA expression in comparison to non-TE genes. The majority of the TEs were silenced, as demonstrated by higher levels of small RNAs and a lack of mRNA MPSS data. When TEs were expressed, their activity was usually limited to just one or a few of the mRNA libraries. When we examined TE expression at the whole-genome level and across the complete mRNA dataset, we observed that most activity was contributed by a few highly expressed transposable elements. These TEs were characterized by their low copy number and few matching small RNAs. Our results help define the relationship between gene expression and gene silencing for TEs, and indicate that TE silencing can impact neighboring genes, perhaps via a mechanism of heterochromatin formation and spreading. These data may be used to define active TEs and families of transposable elements that continue to shape plant genomes.

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Acknowledgments

This work was supported by US National Science Foundation awards 0321437 (B.C.M. and G.-l.W.) and 0439186 (B.C.M.), and US Department of Agriculture 2005-35064-15326 (B.C.M.).

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Authors and Affiliations

  1. Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19711, USA

    André Beló, Kan Nobuta & Blake C. Meyers

  2. Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA

    Kan Nobuta, Prakash E. Janardhanan & Blake C. Meyers

  3. Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA

    R. C. Venu & Guo-liang Wang

Authors
  1. André Beló
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  2. Kan Nobuta
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  3. R. C. Venu
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  4. Prakash E. Janardhanan
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  5. Guo-liang Wang
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  6. Blake C. Meyers
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Correspondence to Blake C. Meyers.

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Communicated by: Elizabeth Ainsworth

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Beló, A., Nobuta, K., Venu, R.C. et al. Transposable Element Regulation in Rice and Arabidopsis: Diverse Patterns of Active Expression and siRNA-mediated Silencing. Tropical Plant Biol. 1, 72–84 (2008). https://doi.org/10.1007/s12042-007-9008-4

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  • DOI: https://doi.org/10.1007/s12042-007-9008-4

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