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TE composition of human long noncoding RNAs and their expression patterns in human tissues

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Abstract

High-throughput sequencing analyses have revealed that transposable elements (TEs) comprise approximately half of the human genome and frequently involved in genomic rearrangements and instability by various mechanisms. Interestingly, many noncoding RNAs (ncRNAs) contain TEs and the TE-containing ncRNAs that have been implicated in cellular processes and various diseases in mammals. In this study, we retrieved 94 human long noncoding RNAs (lncRNAs; >200 nucleotides in length) from lncRNAdb and analyzed TEs which are embedded within the lncRNAs, focusing on their chromosomal distribution. The result showed that TEs occupy ~27 % of the lncRNA transcripts in mass and lncRNA containing TEs are enriched in human chromosome 11. We further analyzed subfamily of the TEs and found that most of the TEs belong to AluSx and L1 which are the most successful TE subfamilies in the human genome. Numerous lncRNAs have been reported to be expressed in a cell-type specific manner. Thus, using reverse transcription PCR with specific primers for the lncRNAs, we examined their expression pattern in human normal tissues and cancer cells. Most of the lncRNAs were universally amplified from 20 different types of normal human tissues but some of them displayed tissue-specific expression. Especially, 11 lncRNAs were expressed only in human cancer cells, implying the possibility of their involvement in carcinogenesis.

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Acknowledgments

The present work was conducted with funding from the Research Fund of Dankook University in 2013.

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The authors declare 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

    Donghee Kang, Yun-Ji Kim, Kwonho Hong & Kyudong Han

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

    Yun-Ji Kim & Kyudong Han

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  1. Donghee Kang
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Correspondence to Kyudong Han.

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Kang, D., Kim, YJ., Hong, K. et al. TE composition of human long noncoding RNAs and their expression patterns in human tissues. Genes Genom 37, 87–95 (2015). https://doi.org/10.1007/s13258-014-0232-7

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