FY2021 Annual Report

Plant Epigenetics Unit
Associate Professor Hidetoshi Saze

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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 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 
  • Matin Miryeganeh, Researcher
  • Leonardo Furci, Researcher
  • Jeremy Berthelier, Researcher
  • Atsushi Shimada, Researcher
  • Hiroki Tsutsui, Researcher (JSPS PD)
  • Oscar Juez Neira, Ph.D. Student
  • Munissa Sadykova, Ph.D. Student
  • Yoshiko Harukawa, Technical Staff
  • Tomoe Shimazaki, Technical Staff
  • Yoko Fujitomi, Research Administrator

2. Collaborations

2.1 Genome analysis of Fukugi tree in Okinawa

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

2.2 Okinawa Functional Rice project

  • Type of collaboration: Joint research
  • Researchers: Onna Village

3. Activities and Findings

3.1 Decoding the genome and epigenome of mangrove Bruguiera gymnorhiza 

Mangroves are adapted to harsh environments, such as high ultraviolet (UV) light, lownutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources.

We performed a de novo genome assembly and in natura epigenome analyses of the mangroveBruguiera gymnorhiza, one of the dominant mangrove species. The 309 Mb of the genome is predicted to encode 34403 genes and has a repeat contentof 48%. Depending on its growing environment, the natural B.gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. 

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Figure 1. (a) A cladogram of plant species including Bruguiera gymnorhiza. (b) Synteny blocks between B.gymnorhiza and Kandelia obovata (yellowribbons), and B.gymnorhiza and Rhizophora apiculata (light blue ribbons) genomes. Figures are adapted from Miryeganeh et al., 2022.   Moreover, high-salinity environments induced genome-wide DNA hypermethylationof transposable elements (TEs) in the B.gymnorhiza, suggesting robust epigenome regulation of TEs in the B.gymnorhiza genome under high-salinity environments. The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating natural environments.      
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Figure 2. (a) A Circos plot showing cytosine methylation levels of the 10 longest scaffolds (> 5 Mb) of Bruguiera gymnorhiza. The outermost circle shows the 10 scaffolds. The next six circles represent the DNA methylation levels in brackish (B) and saline (S) conditions for CG (0 to 1), CHG (0 to 1), and CHH (0 to 0.2) contexts (H can be A, or C, or T) in the natural environment. The first and second innermost circles show the density of genes (black) and transposable elements (TEs; orange), respectively. (b) (Left) Metaplots of cytosine methylation levels in CG, CHG, and CHH contexts for genes and TEs in brackish and saline conditions in the natural environment. (Right) Violin plots showing levels in CG, CHG, and CHH contexts for genes and TEs in brackish and saline conditions in the natural environment. Figures are adapted from Miryeganeh et al., 2022.

4. Publications

4.1 Journals

  1. Irei A, Miryeganeh M, Tamashiro M, Saze H, Urasaki N, Tarora K. Development of a male specific genetic marker for Garcinia subelliptica Merr. tree.  J For Res. 2021, 1-8. doi.org/10.1080/13416979.2021.1897060.
  2. Miryeganeh M, Saze H. De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza). Int J Mol Sci. 2021 Sep 13;22(18):9874. doi: 10.3390/ijms22189874.
  3. Miryeganeh M, Saze H. The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae). Int J Mol Sci. 2021 Nov 4;22(21):11964. doi: 10.3390/ijms222111964.
  4. Miryeganeh M, Marlétaz F, Gavriouchkina D, Saze H. De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza.
    New Phytol. 2022 Mar;233(5):2094-2110. doi: 10.1111/nph.17738. Epub 2021 Oct 16.
    PMID: 34532854

4.2 Books and other one-time publications

  1. (Co-author) Saze H. Chaptor 10 "Epigenetics". Encyclopedia of genetics. Origin of inheritance and diversity. (Japanese). Maruzen-publishing. 28Jan2022.

4.3 Oral and Poster Presentations

  • (Invited talk) Saze H. Epigenetic regulation of intragenic transposons impacts gene transcription in plants. NIG Transposon meeting, National Institute of Genetics, Japan. August 26-27, 2021.
  • (Invited symposium presentation) Saze H, “Plant stress response and epigenetic inheritance”. Annual meeting of the Genetics Society of Japan. 9 Sep. 2021, Tokyo, Japan.
  • (Invited seminar) Saze H, “Epigenetic regulation of intragenic transposons and gene transcription in plant genomes.” Seminar series, Grant-in-Aid for Scientific Research on Innovative Areas “Replication of Non-Genome”. Oct 10, 2021.
  • (Invited symposium presentation) Saze H, “Epigenetic regulation of intragenic transposons and gene transcription in plant genomes”. The 44th Annual meeting of Molecular Biology Society of Japan, Yokohama, Japan. Dec 12, 2021.

5. Intellectual Property Rights and Other Specific Achievements

Registration of a new rice strain approved by Ministry of Agriculture, Forestry and Fisheries: Onna-OIST-2020, No. 2868. Oct 2021.

6. Meetings and Events

Nothing to report.

7. Other

Nothing to report.