FY2019 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 environmental 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)

2.4 Functional Okinawa Rice Project

  • Type of collaboration: Joint research
  • Collaborator: Onna village



3. Activities and Findings

3.1 Epigenetic regulation of intronic transposable elements in the rice genome.

Intron of eukaryotic genomes accumulate many Transposable Elements (TEs) and repeats. However, the distribution of TEs in the intragenic regions, and their contributions to genetic diversity and evolution in plant genomes, remain poorly understood.We investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome, where TEs comprise 35% of the genome. We found that over 10% of rice genes contain introns associated with repressive heterochromatin. Genes with heterochromatic introns tend to show tissue-specific expression patterns, and are also implicated in the development and responses to environmental stimuli. The conserved protein OsIBM2 is required for proper transcription of genes with heterochromatic introns. We also found that heterochromatic introns evolve rapidly compared to non-heterochromatic introns. Our study indicates that heterochromatin is a common feature in transcribed genes involved in basal functions in the rice genome (Espinas et al., 2020). 



Figure 1: Genes with heterochromatic intron in the rice genome.

Figure 2: Accumulation of DNA methylation in the rice intron

Figure 3: Loss of OsIBM2 causes developmental defects in rice



4. Publications

4.1 Journals

  1. Espinas NA, Tu LN, Furci L, Shimajiri Y, Harukawa Y, Miura S, Takuno S, Saze H. (2020). Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome. PLoS Genet. Mar 18;16(3):e1008637. doi: 10.1371/journal.pgen.1008637
  2. Espinas NA, Villar-Briones A, Roy MC, Saze H. (2020). Rice Histone Propionylation and Generation of Chemically Derivatized Synthetic H3 and H4 Peptides for Identification of Acetylation Sites and Quantification. Methods Mol Biol. 2093:81-92. doi: 10.1007/978-1-0716-0179-2_6.
  3. (Review)  Miryeganeh M, Saze H. (2020). Epigenetic inheritance and plant evolution. Population Ecology 62 (1), 17-27.

4.2 Books and other one-time publications

  1. (Japanese) Saze H. Epigenetic regulation of plant genomes. (2020) Gene & Medicine 10(1) 8,154 - 158. 

4.3 Oral and Poster Presentations

  1. (Oral presentation) Saze H. "Epigenetic regulation of intragenic transposons and gene transcription in plants" Academia Sinica x OIST Joint Symposium 2019, April 18, 2019, OIST, Japan.
  2. (Oral presentation) Saze H. "Epigenetic regulation of intronic transposons in plants" The 91st Annual Meeting of the Genetics Society of Japan. September 13, 2019, Fukui, Japan.
  3. (Oral presentation) Saze H. "Epigenetic regulation of transposable elements and envrionmental responses in plants" The 83rd Annual Meeting of the Botanical Society of Japan, Sendai 2019.
  4. (Oral & poster presentations) Tu LN. Dissecting genetic codes of plant epigenomes with convolutional neural network. The 13th Annual Meetingof the Japanese Scoiety for Epigenetics. May 28, 2019, Yokohama, Japan.
  5. (Oral presentation) Tu LN, Saze H. "Learning regulatory codes of plant epigenomes with convolutional neural networks", The 3rd meeting of the Plant Epigenetics Consortium in Japan, Mishima, Japan, August 2019.
  6. (Poster presentation) Tu LN, Saze H. "A deep-learning approach to dissecting functional impact of DNA methylation in plants", ISMB/ECCB 2019, Basel, Switzerland, July 2019.
  7. (Poster presentation) Miryeganeh M, Saze H. "Transcriptomic and Epigenomic Responses of Mangrove Trees to Different Stressful Environments" Joint Meeting Acadian Entomological Society Entomological Society of Canada Canadian Society for Ecology and Evolution. Fredericton, NB. August 18 – 21, 2019.
  8. (Poster presentation) Miryeganeh M, Saze H. "Transcriptomic and Epigenomic Responses of Mangrove Trees to Different Stressful Environments" Joint Meeting of the Society for Tropical Ecology (gtö) and the British Ecological Society Tropical Ecology Group (BESTEG)- Edinburgh, UK, 8-12 April 2019
  9. (Oral presentation) Furci L. "The role of DNA methylation in Arabidopsis immunity". The 3rd meeting of the Plant Epigenetics Consortium in Japan, Mishima, Japan, August 2019.
  10. (Oral presentation) Berthelier J. "PiRATE v2: detection, classification and annotation of transposable elements of non-model organisms". The 3rd meeting of the Plant Epigenetics Consortium in Japan, Mishima, Japan, August 2019.

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 (Invited Seminar) "Light controls protein localization through phytochrome-mediated alternative promoter selection in Arabidopsis"

  • Date: Monday, April 15, 2019 - 10:00 to 11:00
  • Venue: C700, Lab3
  • Speaker:  Prof. Tomonao Matsushita (Faculty of Agriculture, Kyushu University, Japan)

6.2 (Invited Seminar) "Organic chemistry for epigenetic studies"

  • Date: Monday, July 1, 2019 - 09:30 to 10:30
  • Venue: C015, Lab1
  • Speaker:  Prof. Akimitsu Okamoto, Research Center for Advanced Science and Technology, The University of Tokyo

6.3 (Invited Seminar) "Genomic Medicine: From Human to Plant"

  • Date: Wednesday, October 2, 2019 - 15:00 to 16:00
  • Venue: B700, Lab3
  • Speaker:   Prof. Bin Tean Teh, MD, PhD , National Cancer Centre of Singapore

6.4 (Invited Seminar) "Epigenetic Variation Plays a Role in Plant Adaptation"

  • Date: Friday, October 18, 2019 - 10:00 to 11:00
  • Venue: C700, Lab3
  • Speaker:  Prof. Ueli Grossniklaus, Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland

6.5 (Invited Seminar) "Detection of somatic variations in the human brains at the single cell level"

  • Date: Monday, January 20, 2020 - 16:00 to 17:00
  • Venue: C015, Lab1
  • Speaker:  Prof. Miki Bundo, Department of Molecular Brain Science, Kumamoto University, Kumamoto, Japan / PRESTO, Japan Science and Technology Agency, Saitama, Japan

7. Other

Nothing to report.