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Expression analysis of LTR-derived miR-1269a and target gene, KSR2 in Sebastes schlegelii

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Abstract

Background

Sebastes schlegelii are an important species of fish found in the coastal areas of the Korea with significant commercial importance. Most studies thus far have been primarily focused on environmental factors; behavioural patterns, aquaculture, diseases and limited genetic studies with little to none related to either microRNAs (miRNAs) or transposable elements (TE).

Objectives

In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii. Also, we performed luciferase reporter assay in HINAE cells.

Methods

UCSC Genome Browser (https://genome.ucsc.edu/) was used to examine which TE is associated with miR-1269a. For the target genes for miR-1269a, the target genes associated with the miRNA were identified using miRDB (http://www.mirdb.org/) and TargetScan 7.1 (http://www.targetscan.org/vert_71/). A two-step miRNA kit, HB miR Multi Assay Kit™ System. I was used for the analysis of TE-derived miRNA expression patterns. The 3′UTR of KSR2 gene was cloned into the psiCHECK-2 vector. Subsequently co-transfected with miR-1269a mimics to HINAE cells for luciferase reporter assay.

Results

MiR-1269a was found to be derived from LTR retrotransposon, MLT2B. LTR-derived miR-1269a was highly expressed in the muscle, liver and gonad tissues of Sebastes schlegelii, but KSR2 revealed high expression in the brain. Co-transfection of KSR2 and miR-1269a mimic to HINAE cells showed high activity of miR-1269a in relation to KSR2.

Conclusion

LTR-derived miR-1269a showed enhancer activity with relation to KSR2 in Sebastes schlegelii. The data may be used as a foundation for further investigation regarding correlation of miRNA and target genes in addition to other functional studies of biological significance in Sebastes schlegelii.

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Acknowledgements

This research was a part of the project titled “Omics based on fishery disease control technology development and industrialization (20150242) funded by the Ministry of Oceans and Fisheries, Korea.

Funding

This research was a part of the project titled “Omics based on fishery disease control technology development and industrialization (20150242) funded by the Ministry of Oceans and Fisheries, Korea.

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Author notes

  1. Jennifer Im and Woo Ryung Kim contributed equally.

Authors and Affiliations

  1. Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea

    Jennifer Im, Woo Ryung Kim, Hee-Eun Lee & Heui-Soo Kim

  2. Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea

    Jennifer Im, Woo Ryung Kim, Hee-Eun Lee & Heui-Soo Kim

  3. Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea

    Ahran Kim & Do-Hyung Kim

  4. Department of Biochemistry, College of Korean Medicine, Dong-eui University, Busan, 47340, Republic of Korea

    Yung Hyun Choi

  5. Department of Parasitology and Genetics, College of Medicine, Kosin University, Busan, 49267, Republic of Korea

    Hee-Jae Cha

  6. Department of Chemistry, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea

    Suhkmann Kim

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  1. Jennifer Im
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Correspondence to Heui-Soo Kim.

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Conflict of interest

Jennifer Im, Woo Ryung Kim, Hee-Eun Lee, Ahran Kim, Do-Hyung Kim, Yung Hyun Choi, Hee-Jae Cha, Suhkmann Kim and Heui-Soo Kim declare that we have no conflict of interest.

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All experiments were carried out in accordance with the guidelines and regulation approved by Pusan National University-Institutional Animal Care and Use Committee (PNU-IACUC).

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Im, J., Kim, W.R., Lee, HE. et al. Expression analysis of LTR-derived miR-1269a and target gene, KSR2 in Sebastes schlegelii. Genes Genom 42, 55–65 (2020). https://doi.org/10.1007/s13258-019-00880-0

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