Molecular Biology Reports

, Volume 46, Issue 4, pp 3791–3800 | Cite as

Identification and sequencing of the gene encoding DNA methyltransferase 3 (DNMT3) from sea cucumber, Apostichopus japonicus

  • Hyun-Hee Hong
  • Sung-Gwon Lee
  • Jihoon Jo
  • Jooseong Oh
  • Seongmin Cheon
  • Hyun-Gwan Lee
  • Chungoo ParkEmail author
Original Article


The sea cucumber Apostichopus japonicus is well known as a traditional tonic food and as a commercially important cultured aquatic species. This species produces saponins, and has a high potential to cope with environmental stress, such as aestivation, organ regeneration, and wound healing. Recently, several studies have shown that cellular reprogramming and the physiological responses of the sea cucumber to environmental changes, including aestivation, are potentially mediated by epigenetic DNA methylation. The DNA methyltransferase (DNMT)1 and DNMT3 genes are independent participants in the maintenance and de novo methylation of specific sequences. Sea urchin (Strongylocentrotus purpuratus) and starfish (Asterina pectinifera), which belong to the same phylum as A. japonicus, have both DNMT1 and DNMT3 genes. However, it was previously reported that DNMT1 is present, but DNMT3 is absent, in A. japonicus. In the present study, we sequenced the full-length cDNA of the A. japonicus DNMT3 gene. The newly sequenced DNMT3 gene comprises three major conserved domains (Pro-Trp-Trp-Pro (PWWP), plant homeodomain (PHD), and S-adenosylmethionine-dependent methyltransferase (AdoMet-MTase)), indicating that the DNMT3 possibly has de novo DNA methylation catalytic activity. Gene structure and phylogenetic analysis showed that sea cucumber DNMT3 is evolutionarily conserved in the Echinodermata. Next, we demonstrated the conservation of DNMT3 gene expression in sea cucumber and starfish belong to same phylum, echinoderm. Using reverse transcription-polymerase chain reaction, sea cucumber DNMT3 mRNA was detected in testis tissue, but not in other tissues tested, including the respiratory tree, muscle, tentacle, intestine, and ovary. This is inconsistent with previous reports, which showed the expression of DNMT3 in ovary, but not in testis of the starfish A. pectinifera, indicating the tissue- and species-specific expression of DNMT3 gene. Although further studies are needed to clarify the epigenetic regulatory mechanisms of DNMT3 and its application to the aquaculture industry, our findings may provide insights into the sea cucumber biology.


Sea cucumber Apostichopus japonicus DNA methylation DNMT3 RACE-PCR Phylogenetic analysis 



This research was supported by the Collaborative Genome Program (No. 20180430), and “Development of methods for controlling and managing marine ecological disturbance-causing and harmful organisms” (MEDHO), and “Research center for fishery resource management based on the information and communication technology (ICT)” of the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries of the Republic of Korea to C.P.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human subject or animals performed by any of the authors.

Supplementary material

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Supplementary material 1 (TIFF 17582 kb)
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Supplementary material 2 (TIFF 4096 kb)
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Supplementary material 3 (TIFF 3072 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.School of Biological Sciences and TechnologyChonnam National UniversityGwangjuRepublic of Korea
  2. 2.Department of Oceanography, Marine Ecological Disturbing and Harmful Organisms Research CenterChonnam National UniversityGwangjuRepublic of Korea

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