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Evolutional and functional analysis of four microRNAs derived from transposable elements

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Abstract

Transposable elements (TEs) are interspersed in the host genomic regions, and induce various effects to the host. Recent study shows TE sequences can provide microRNA (miRNA) sequences which have a crucial role in the organisms by silencing target mRNAs. In this study, 14 TE-derived miRNAs were identified by overlapping >50 % with expressed sequence tag. Among them, miR-330, miR-648, miR-1254, and miR-1825 were examined regarding their expression patterns and evolutionary conservation in various species. MiR-330 and miR-648 were highly expressed in the bone marrow and cerebellum tissues, while miR-1825 showed high expression in the fetal liver tissue. Additionally, MiR-1254 showed dominant expression in the skeletal muscle. These TE-derived miRNAs showed an inhibitory effect on the expression of their target genes, MLL2 and ARHGEF12. These findings confirmed that TEs play important roles to regulate gene expression by providing miRNA sequences and they may contribute to the evolution of biological complexity in human genome.

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Acknowledgments

The present research was conducted by the research fund of Dankook University in 2014.

Conflict of interest

The author declares that there is no conflict of interests exists in this paper.

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Authors and Affiliations

  1. Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea

    Yun-Ji Kim

  2. DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan, 330-714, Republic of Korea

    Yun-Ji Kim

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Correspondence to Yun-Ji Kim.

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13258_2014_255_MOESM1_ESM.pptx

Fig. S1 Prediction of RNA secondary structure of chimeric ESTs overlapped with four TE-derived miRNAs. (a) T54717.1 derived miR-330, (b) CV312382.1 derived miR-648, (c) BX111415.1 derived miR-1254, and (d) BF568983.1 derived miR-1825. Green and yellow line indicate precursor miRNA and mature miRNA sequences, respectively. (PPTX 479 kb)

13258_2014_255_MOESM2_ESM.pptx

Fig. S2 Secondary structure of potential miRNAs derived from paralogs of mir-1254. Predicted miRNAs (paralogs) derived from AluJr (miR-1254) and their secondary structures were predicted by using miRNAFinder. Left (blue) and right (red) lines indicate predicted mature miRNAs. (PPTX 287 kb)

13258_2014_255_MOESM3_ESM.pptx

Fig. S3 Complementary sequences between 3′UTR of target gene and mature miRNA. (a) The MLL2 gene targeted by miR-330 and miR-1254. (b) The ARHGEF12 gene targeted by miR-648 and miR-1825. Using RNAhybrid, secondary structure and free energy of hybridization were predicted (Rehmsmeier et al. 2004). Grey bar on secondary structure indicates seed sequence. (PPTX 48 kb)

13258_2014_255_MOESM4_ESM.pptx

Fig. S4 Sequence of seed region in target gene. Through sequencing analysis, seed region of TE-derived miRNAs in the MLL2 (a) and ARHGEF12 genes (b) were confirmed. (PPTX 117 kb)

Supplementary material 5 (XLSX 45 kb)

Supplementary material 6 (XLSX 12 kb)

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Kim, YJ. Evolutional and functional analysis of four microRNAs derived from transposable elements. Genes Genom 37, 161–171 (2015). https://doi.org/10.1007/s13258-014-0255-0

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  • DOI: https://doi.org/10.1007/s13258-014-0255-0

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