Expression and promoter activity of endogenous retroviruses in the Olive flounder (Paralichthys olivaceus)

Nam, Gyu-Hwi; Gim, Jeong‐An; Lee, Hee-Eun; Kim, Woo Jin; Jung, Hyungtaek; Kim, Won; Kim, Heui‐Soo

doi:10.1007/s13258-016-0404-8

Cited by 2 publications

(3 citation statements)

References 40 publications

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“…The ERV9 found in olive flounder has well conserved LTRs, including gag , pol , env and ppt sequences. A previous study has shown that OF-ERV5 also has well-conserved sequences among olive flounder and confirmed the promoter activity of OF-ERV5, 9 and 10 in both HINAE and HepG2 cell lines 19 . The present study is mainly focused on the OF-ERV9-LTR, another highly conserved and widely spread OF-ERV in olive flounder and supports the idea that both TEs truly are “jumping genes”.…”

Section: Discussionsupporting

confidence: 63%

“…Alternative promoter and enhancer activity are an additional function of TE, which can act as both a promoter and an enhancer by inserting itself into specific genes 9,28,29 . The present study suggests that OF-ERV9-LTR mainly has enhancer activity, despite having a weak promoter activity 19 . Moreover, TEs provide binding sites for TFs, thereby greatly influencing gene regulation 18,30–32 .…”

Section: Discussionmentioning

confidence: 48%

“…Furthermore, studies have shown that species-specific ERV enhancer activity is generally restricted to hypomethylated tissues, suggesting that ERV families are an important mediator in evolutionary regulation 18 . In the case of olive flounder, chromosome 5-derived OF-ERV5-LTR has shown promoter activity in HepG2 and HINAE cells which prompted us to investigate the role of OF-ERV9-LTR in this study 19 .…”

Section: Introductionmentioning

confidence: 99%

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Characterization of the Long Terminal Repeat of the Endogenous Retrovirus-derived microRNAs in the Olive Flounder

Lee

et al. 2019

Sci Rep

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Endogenous retroviruses (ERVs) have been identified at different copy numbers in various organisms. The long terminal repeat (LTR) element of an ERV has the capacity to exert regulatory influence as both a promoter and enhancer of cellular genes. Here, we describe olive flounder (OF)-ERV9, derived from chromosome 9 of the olive flounder. OF-ERV9-LTR provide binding sites for various transcription factors and showed enhancer activity. The OF-ERV9-LTR demonstrates high sequence similarity with the 3′ untranslated region (UTR) of various genes that also contain seed sequences (TGTTTTG) that bind the LTR-derived microRNA(miRNA), OF-miRNA-307. Additionally, OF-miRNA-307 collaborates with transcription factors located in OF-ERV9-LTR to regulate gene expression. Taken together, our data facilitates a greater understanding of the molecular function of OF-ERV families and suggests that OF-miRNA-307 may act as a super-enhancer miRNA regulating gene activity.

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Section: Discussionsupporting

confidence: 63%

Section: Discussionmentioning

confidence: 48%

Section: Introductionmentioning

confidence: 99%

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Characterization of the Long Terminal Repeat of the Endogenous Retrovirus-derived microRNAs in the Olive Flounder

Lee

et al. 2019

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Identification of transposable elements fused in the exonic region of the olive flounder genome

et al. 2018

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Transposable elements (TEs) are mobile genetic sequences that comprise a large portion of vertebrate genomes. The olive flounder (Paralichthys olivaceus) is a valuable marine resource in East Asia. The scope of most genomic studies on the olive flounder is limited to its immunology as their focus is the prevention of mass mortality of this species. Thus, for a broader understanding of the species, its genomic information is consistently in demand. Transcripts sequences were acquired from transcriptome analysis using gill tissues of 12 olive flounders. Distribution of TEs inserted in exonic region of the olive flounder genome was analyzed using RepeatMasker ( http://www.repeatmasker.org/ ). We found 1140 TEs in the exonic region of the genome and long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs) insertions occurred with forward orientation preferences. Transposons belonging to the hAt, Gypsy, and LINE 1 (L1) subfamilies were the most abundant DNA transposons, LTRs, and long interspersed elements (LINEs), respectively. Finally, we carried out a gene ontology analysis to determine the function of TE-fused genes. These results provide some genomic information about TEs that is useful for future research on changes in properties and functions of genes by TEs in the olive flounder genome.

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Expression and promoter activity of endogenous retroviruses in the Olive flounder (Paralichthys olivaceus)

Cited by 2 publications

References 40 publications

Characterization of the Long Terminal Repeat of the Endogenous Retrovirus-derived microRNAs in the Olive Flounder

Characterization of the Long Terminal Repeat of the Endogenous Retrovirus-derived microRNAs in the Olive Flounder

Identification of transposable elements fused in the exonic region of the olive flounder genome

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