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Complexity and Specificity of Precursor microRNAs Driven by Transposable Elements in Rice

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Abstract

In eukaryotes, small noncoding RNA molecules of 16–29 nucleotides in length play crucial roles in the regulation of gene expression. Some 377 sequences representing rice pseudo-microRNAs (miRNAs) are available in release 13.0 of the miRBase sequence database (http://microrna.sanger.ac.uk/sequences/index.shtml) and are grouped into 143 families. Most newly deposited miRNA sequences are likely to be species-specific. To understand the relationship between miRNAs and transposable elements (TEs) in rice, the RepeatMasker application (http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker) was used to screen single-stranded precursor miRNA (pre-miRNA) sequences. This analysis revealed that 33.1% of miRNAs and 36.4% of miRNA families are associated with interspersed repeats, and most of them are species-specific. Furthermore, multiple miRNA families can be encoded by the same TE class. Alignment analysis revealed that miR439 originated from an MuDR4-OS TE, which amplified and diversified in the genome as an inverted repeat of the core sequence followed by multiple repeats. Multiple copies of miR445 and its complexity originate from and are driven by the DNA/Tourist TE class. These results provide an important contribution to the elucidation of TE-driven mechanisms that regulate the species specificity and complexity of rice miRNAs.

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Acknowledgements

We thank Dr. Lida Zhang (Plant Biotechnology Research Center, Shanghai Jiaotong University, Shanghai, China) for giving some valuable advice. This research is supported by National Natural Science Foundation of China (30830071) and Shanghai Rising-Star Program (07QA14045).

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Authors and Affiliations

  1. Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Germsperm Resources Division (Shanghai), National Key Laboratory of Crop Genetic Improvement, Shanghai, 201106, China

    Shunwu Yu, Jiajia Li & Lijun Luo

  2. Huazhong Agricultural University, Wuhan, 430070, China

    Jiajia Li & Lijun Luo

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  1. Shunwu Yu
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  2. Jiajia Li
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  3. Lijun Luo
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Correspondence to Lijun Luo.

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Supplement Table 1

List of microRNA families and its members in rice (XLS 72 kb)

Supplement Table 2

Rice microRNA genes derived from interspersed repeats (XLS 41 kb)

Supplement Table 3

Arabidopsis microRNA genes derived from interspersed repeats (XLS 19 kb)

Supplement Table 4

Pre-miR439, pre-miR439*, and their homologs in rice genome (XLS 20 kb)

Supplement Table 5

Pre-miR445 and their homologs in rice genome (XLS 39 kb)

Supplement Fig. 1

Potential secondary structures of precursor miR439i and its homologs in rice genome. The genome loci of miR439i1-5 were shown in Supplement Table 4. The bars indicate the responding miR439i sequence (GIF 206 kb)

High resolution (TIFF 1239 kb)

Supplement Fig. 2

Alignment of miR439 gene region in rice genome. The box and broken box indicated the mature sequence domain and the complementary sequences, respectively. The underline and broken lines indicated the matrue sequence of miR439j and its complementary sequence (GIF 1025 kb)

High resolution (TIFF 1695 kb)

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Yu, S., Li, J. & Luo, L. Complexity and Specificity of Precursor microRNAs Driven by Transposable Elements in Rice. Plant Mol Biol Rep 28, 502–511 (2010). https://doi.org/10.1007/s11105-009-0175-3

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