FY2018 Annual Report

Plant Epigenetics Unit
Associate Professor  Hidetoshi Saze


Epigenetic Regulation of Genes and Transposable Elements in Plant Genomes

We are studying epigenetic regulation of genes and transposable elements (TEs) in plant genomes. Genome defense mechanisms in plants repress TEs by epigenetic modifications, such as DNA cytosine methylation, small RNAs, and modifications of histone proteins. In contrast, these repressive epigenetic modifications are generally excluded from actively transcribed genes. The major goal of our research is to understand how epigenetic mechanisms distinguish gene and TE sequences, how they deposit specific chromatin modifications at the targets, and to elucidate their biological significance in adaptation and genome evolution. 

1. Staff

  • Hidetoshi Saze, Associate Professor 
  • Le Tu Ngoc, Researcher
  • Matin Miryeganeh, Researcher (JSPS PD)
  • Leonardo Furci, Researcher
  • Jeremy Berthelier, Researcher
  • Tomohito Wauke, Student
  • Yoshiko Harukawa, Technical Staff
  • Saori Miura, Technical Staff
  • Yoko Fujitomi, Research Administrator

2. Collaborations

2.1 Analysis of transposable elements in plant genomes

  • Type of collaboration: Joint research
  • Researchers:
    • Prof. Shohei Takuno, Department of Evolutionary Studies of Biosystems School of Advanced Sciences, SOKENDAI​

2.2 Genome analysis of Fukugi tree in Okinawa

  • Type of collaboration: Joint research
  • Researchers:
    • Ms. Ayaka Irei, Okinawa Prefectural Agricultural Research Center

2.3 Epigenetic regulation of immune response in rice

  • Type of collaboration: Joint research
  • Researchers:
    • Dr. Nino Espinas, Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science (CSRS)


3. Activities and Findings

3.1 Epigenetic regulation of intragenic transposons

Genomes of animals and plants contain a large number of transposable elements (TEs). TEs often transpose into genic region and affect expression of surrounding genes. The intragenic TEs mostly reside in intron, and as intergenic TEs, they are targeted by repressive epigenetic marks for transcriptional silencing. Expression of TE-bearing genes is generally co-repressed with the silenced TEs, while in some cases it rather enhances splicing and transcript elongation. Genomes have evolved molecular mechanisms that allow the presence of silenced TEs within transcriptionally permissive chromatin environments. Epigenetic modulation of intragenic TEs often contribute to gene regulation, phenotypes of individuals, and genome evolution. 



Figure 1: Transcriptional defects caused by insertion of TEs into intronic region of genes. (A) Premature polyadenylation. (B) Incorporation of TE sequence as exonization. (C) Abberant transcripts from TE promoters (D) Co-repression of associated genes. The figure is adopted from Saze H. 2018.


4. Publications

4.1 Journals

  1. (Review) Saze H. (2018). Epigenetic regulation of intragenic transposable elements: a two-edged sword. J Biochem. 164(5):323-328.

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations


1. (Invited talk) Saze H. Epigenetic regulation of intragenic transposons and gene transcription in plants. Epigenetics and chromatin, Cold Spring Harbor Laboratory, US. Sep 11-15, 2018. 

2. (Invited talk) Saze H. Epigenetic regulation of intragenic transposons impacts gene transcription in plants. NIG meeting Macro Ecology and Genetics, National Institute of Genetics, Japan. April 14-15, 2018.

3. (Poster presentation) Espinas NA. CBP-dependent regulation in rice innate immunity. The 12th Annual Meeting of the Japanese Society for Epigenetics,  Sapporo, Japan, May 25, 2018.

4. (Poster presentation) Miyazaki Y. Impact of circadian clock on DNA methylation and gene expression in Arabidopsis. The 12th Annual Meeting of the Japanese Society for Epigenetics,  Sapporo, Japan, May 25, 2018.

5. (Poster presentation) Osabe K. Epigenetic regulation of intronic transgene. The 12th Annual Meeting of the Japanese Society for Epigenetics,  Sapporo, Japan, May 25, 2018.

6. (Poster presentation) Miryeganeh M. TRANSCRIPTOMIC RESPONSES OF MANGROVE TREES TO DIFFERENT STRESSFUL ENVIRONMENTS. Canadian Society of Ecology and Evolution Annual Meeting 2018, Canada, July 20, 2018.

7. (Poster presentation) Miryeganeh M.De novo RNA assembly of mangroves and transcriptomic responses to different natural habitats​. Annual Conference Ecological Society of Australia, Brisbane, Australia. Nov. 27, 2018.

8. (Poster presentation) Le TN. Learning genomic determinants of plant epigenomes by convolutional neural network. The 11th RECOMB/ISCB Conference on Regulatory and System Genomics, NY, US, Dec 9, 2018.



    5. Intellectual Property Rights and Other Specific Achievements

    Nothing to report

    6. Meetings and Events

    6.1 (Invited Seminar) The epigenetic field: its formation mechanisms and clinical applications

    • Date: July 13, 2018
    • Venue: C700 lab3.
    • Speaker: Dr. Toshikazu Ushijima
      Chief, Division of Epigenomics, National Cancer Center Research Institute.


    7. Other

    Nothing to report.