FY2013 Annual Report

Plant Epigenetics Unit

Assistant Professor Hidetoshi Saze


Our goal is to understand underlying molecular mechanisms of regulation of epigenetic modifications in organismal genomes. We are currently using model plants Arabidopsis and rice to study factors that regulate differential distributions of epigenetic modifications between genes and transposable elements (TEs). We also participate in an Okinawan R&D cluster program in which we use genomic information from rice to develop a rice strain useful for prevention and improvement of life-style-related diseases.

1. Staff

  • Dr. Hidetoshi Saze, Principle Investigator  
  • Dr. Yuji Miyazaki, Researcher
  • Dr. Ngoc Tu LE, Researcher
  • Dr. Kenji Osabe, Researcher
  • Ms. Yoshiko Harukawa, Technical Staff
  • Dr. Saori Miura, Technical Staff
  • Ms. Yasuka, Shimajiri, Technical Staff
  • Ms. Yoko Fujitomi, Research Administrator
  • Mr. Nino Espinas, Student

2. Collaborations 

Nothing to report

3. Activities and Findings 

3.1 Regulation of intragenic TEs in Arabidopsis

Genomes of vertebrates and plants contain a substantial number of transposable elements (TEs), which are silenced by repressive epigenetic modifications, such as cytosine methylation and methylation of lysine 9 of histone H3 (H3K9me), that are essential for formation of inactive chromatin structures called heterochromatin.  In contrast, these modifications are generally excluded from active genes.  A potential complication is that active genes sometimes contain TEs within their transcribed regions, particularly in higher eukaryotes with large genomes.  However, regulation of genes containing intragenic TEs remains largely unexplored.

We found that in Arabidopsis, transcription of genes containing intragenic TEs requires a novel factor named IBM2 (Saze et al., 2013).  IBM2 specifically recognizes heterochromatin formed in genic regions, but not in intergenic TEs (Figure1).  Furthermore, IBM2 eventually masks effects of genetic variations present among Arabidopsis natural accessions, which are created by TE insertion/deletion within gene bodies.  Our results reveal a novel epigenetic mechanism that masks deleterious effects of intragenic heterochromatin, providing evolutionary sources for genetic and epigenetic variations in the genome.

Figure 1. IBM2 specifically recognizes at intragenic TEs, but not intergenic TEs.  Chromatin Immuno-Precipitation (ChIP) was performed to detect localization of IBM2 protein at gene and TE sequences.  Red bar represents enrichment of IBM2 proteins at the sequences indicated below.  IBM2 promotes full-length transcription of genes containing TEs with heterochromatic epigenetic modifications.

3.2 Okinawa functional rice project

We are currently trying to breed a functional rice strain named “Amiromochi” in Okinawa, supported by the Research & Development Cluster program of Okinawa Prefecture.  This rice strain accumulates digestion-resistant starch that does not easily break down into glucose.  This trait would be useful for improvement or prevention of life-style-related diseases such as obesity and diabetes, which are serious problems in Okinawa.  However, at present, Amiromochi rice yields much smaller crops in Okinawa than in mainland Japan.  To solve this, we are trying to improve genetic traits, including light and temperature sensitivities, using genomic information obtained with high-throughput sequencers in OIST.  We are also accelerating plant breeding by shortening the life cycle of the rice using plant growth chambers and embryo rescue techniques (Figure 2).

Figure 2.  Breeding of Amiromochi rice in plant growth chamber. Top: Rice plants in growth chamber and growing F1 seeds after a cross. Bottom: Embryo rescue to shorten the life cycle of the rice.



4. Publications 

4.1 Journals 

Saze, H., Kitayama, J., Takashima, K., Miura, S., Harukawa, Y., Ito, T. & Kakutani, T.  Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin. Nature communications 4, 2301, doi:10.1038/ncomms3301 (2013).

4.2 Books and Other One-Time Publications 

(Book chapter: Japanese) Saze, H.  Plant Cell Organization & Epigenetics in Plants, in Visual Reference Book of GENE    Vol.   Chapter2-Section5 & Chapter6-Section8, p34-35 & p134-135, Yushokan (2013).

(Book chapter: Japanese) Saze, H.  Environmental Response and Epigenetic Regulation in Plants, in Key Words in Epigenetics Vol.   Chapter2-Section7, p145-151, Yodosha  (2013).

4.3 Oral and Poster Presentations 

(Invited talk) Saze, H.  Control of intragenic heterochromain, in The 7th Annual Meeting of the Japanese society for Epigenetics, Nara, Japan (2013).

(Poster Presentation) Saze, H.  Mechanism for full-length RNA processing of Arabidopsis genes containing heterochromatin, in Gordon Research Conference; Epigenetics, Bryant University, RI, US (2013)

(Invited talk) Saze, H.  Control of intragenic heterochromatin in Arabidopsis, in The 85th annual meeting of the genetic society of Japan, Keio University, Yokohama, Japan (2013).

(Invited talk) Saze, H.  Epigenetic control of intragenic transposable elements, in Workshop; Interaction between host and transposable elements, National Institute of Genetics, Mishima, Shizuoka, Japan (2013).

(Invited lecture) Saze, H.  Introduction to Epigenetics, Hokkaido University, Sapporo, Hokkaido, Japan (2014).

(Invited talk)  Saze, H.  Control of intragenic heterochromain in Arabidopsis, in The 55th Annual Meeting of the Japanese society of Plant Physiologists, Toyama University, Toyama, Japan (2014).

5. Intellectual Property Rights and Other Specific Achievements 

Nothing to report

6. Meetings and Events 

6.1 Symposium and Workshop 

Workshop organizer : Saze H

  • Title:  Interplay of transposable elements and their hosts
  • Date: September 19, 2013
  • Venue: The 85th Annual Meeting of The Genetics Society of Japan, Hiyoshi Campus, Keio University.
  • Co-organizer: Kenji Ichiyanagi (Kyushu University)

7. Others 

Nothing to report.