FY2017 Annual Report

Plant Epigenetics Unit
Assistant Professor  Hidetoshi Saze

Abstract

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 my 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, Assistant Professor 
  • Yuji Miyazaki, Researcher
  • Kenji Osabe, Researcher
  • Matin Miryeganeh, Researcher
  • Le Tu Ngoc, Researcher
  • Yoshiko Harukawa, Technical Staff
  • Saori Miura, Technical Staff
  • Yoko Fujitomi, Research Administrator
  • Nino Espinas, Ph.D. (obtained in Feb, 2018) 
  • Tomohito Wauke, Student
  • Ruth Thompson, Student

2. Collaborations

3. Activities and Findings

3.1 Intronic Transposons in the plant genomes

We have shown that the genome of Arabidopsis thaliana has many TEs within transcriptional gene units (Saze et al., 2013, Le et al., 2015). However, the A. thaliana genome is still relatively small compared with those of other plant species, and there may be more TEs in gene units in taxa with larger genomes. Thus, we are currently investigating the impact of intragenic TEs and their epigenetic regulation in other plant species, which have larger genomes and are also economically important crops worldwide. 

Figure 1. Genome sizes of plant genomes and TE contents.

 

3.2 Okinawa Functional Rice Project

Since FY2012, we have been working on the “functional rice project in Okinawa”.  The rice strain, “Amiromochi,” accumulates digestion-resistant starch that is not readily catabolized to glucose, which could be useful to improve or prevent life-style-related diseases, such as obesity and diabetes.  We have been breeding new varieties suitable for the eare conducting field tests at a farm in Onna-son, Okinawa, as a collaboration between OIST and Onna-son.

 

Figure 2. New rice strain growing in a farm in Onna-son, Okinawa.

4. Publications

4.1 Journals

Nothing to report

4.2 Books and other one-time publications

  1. Saze H. (2018). Transposon-driven environmental adaptation in plants. (Japanese). Leading Author’s, 7, e001. (Review)

4.3 Oral and Poster Presentations

  1. Saze H. Epigenetic regulation of intragenic transposons impacts gene transcription in Arabidopsis. Cutting Edge Developments in RNA biology for the Control of Gene Expression OIST, Okinawa, Japan. Nov 16, 2017. (Invited talk)
  2. Saze H. Epigenetic regulation of intronic repeats in plants. Taiwan-Japan Plant Biology 2017. Academia Sinica, Taipei, Taiwan. Nov 5, 2017.(Invited talk)
  3. Saze H. Epigenetic regulation of genes and transposable elements in plants. The 33rd Annual Meeting of the Society of Population Ecology. Kyushu University, Fukuoka, Japan. Oct 13, 2017. (Invited talk)
  4. Miyazaki Y, Le, TN, Saze H. Bisulfite sequencing analysis of Arabidopsis circadian clock mutants. Taiwan-Japan Plant Biology 2017. Academia Sinica, Taipei, Taiwan. Nov 4, 2017.(Poster)
  5. Miyazaki Y, Le, TN, Saze H. Identification of differentially methylated regions (DMRs) regulated by circadian clock in Arabidopsis. ConBio2017, Kobe, Japan. Dec 7, 2017. (Poster)
  6. Miryeganeh M, Saze H. TRANSCRIPTOMIC RESPONSES OF MANGROVE TREES TO DIFFERENT STRESSFUL ENVIRONMENTS. European Conference of Tropical Ecology, Paris, France, Mar 28, 2018. (Poster)

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Hosted Seminar 

  1. Dr. Ichiro Hiratani, Team Leader, Laboratory for Developmental Epigenetics, RIKEN CDB, Kobe, Japan. “Single-cell DNA replication timing profiling and the 3D genome organization dynamics”. July 20, 2017.

  2. Prof. Yasunori Aizawa, School of Life Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan. "Functional Genomics for Mammalian Upstream ORFs". Dec 13, 2017.