FY2012 Annual Report

Plant Epigenetics Unit

Assistant Professor Hidetoshi Saze


Genomes of higher eukaryotes contain many transposable elements (TEs), which are generally associated with repressive epigenetic modifications such as DNA cytosine methylation, small RNA production, and modifications of histone proteins. The epigenetic marks, often called heterochromatic epigenetic modifications, are essential for efficient inactivation of TEs. We are exploring the underlying molecular mechanisms of the regulation of epigenetic modifications by using model plants such as Arabidopsis and rice, focusing on epigenetic factors that regulate proper distributions of epigenetic modifications between genes and TEs. Since FY2012, we also participate in an R&D cluster program where we use genome information to improve rice traits for cultivation in Okinawa.

1. Staff

  • Hidetoshi Saze, Assistant Professor
  • Yuji Miyazaki, Researcher
  • Ngoc Tu LE, Resercher
  • Yoshiko Harukawa, Technical Staff
  • Saori Miura, Technical Staff
  • Yasuka, Shimajiri, Technical Staff
  • Yoko Fujitomi, Research Administrator

2. Collaborations

Nothing to report.

3. Activities and Findings

 Regulation of intragenic heterochromatin

We are currently analyzing the Arabidopsis mutants that affect epigenetic regulation of gene and transposable elements (TEs). Genomes of vertebrates and plants contain a substantial number of TEs, which are silenced by repressive epigenetic modifications, such as cytosine methylation and methylation of lysine 9 of histone H3. These modifications are essential for formation of inactive chromatin structures called heterochromatin. 
In the course of our study, we found that heterochromatic epigenetic modifications are commonly found within actively transcribed gene units in both the Arabidopsis and rice genomes. We further found that in Arabidopsis, full-length transcription of genes with intragenic heterochromatin, most of which is formed by TE insertions, requires IBM2 (Increase in Bonsai Methylation 2: Fig1). Our results revealed a novel epigenetic mechanism that masks effects of genetic variations created by TE insertions, allowing evolution of complex genomes with heterochromatic domains having diverse functions. 

Figure 1:Full-length transcription of the gene (AT3G05410) containing heterochromatin is impaired in ibm2 mutant. mRNA reads are indicated with green and red. Reads with dotted lines are mapped across exon-exon boundaries. Note that the inserted TE (ATLINE2) is associated with heterochromatic H3K9 methylation (bottom).


4. Publications

4.1 Journals

  1. (Review) Saze, H. Transgenerational Inheritance of Induced Changes in the Epigenetic State of Chromatin in Plants. Genes Genet Systems 87, No.3, pp. 145-52 (2012).

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  1. (Invited talk) Saze H: Was Lamark Right? Thirteenth Japanese-American Kavli Frontiers of Science Symposium, Irvine, California, US. December 2, 2012.
  2. (Invited lecture) Saze H: Introduction to Epigenetics. Intensive course for Ph.D. students in Ryukyu Univ., Saga Univ., Kagoshima Univ., Naha, Japan. November 7, 2012.
  3. (Invited talk)  Saze H: Epigenetic regulation of gene activity in plants. The 59th Annual Meeting of the Japanese society for food science and technology, Sapporo, Japan. August 30, 2012. 
  4. (Invited seminar) Saze H: Epigenetic control of genes and transposable elements in Arabidopsis thaliana. Max Planck Institute for Plant Breeding Research, Colonge, Germany. June 27, 2012.

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Nothing to report