FY2022 Annual Report

Plant Epigenetics Unit
Professor Hidetoshi Saze

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Abstract

Epigenetic Regulation of Genes and Transposable Elements in Plant Genomes

Our research focuses on investigating the epigenetic regulation of genes and transposable elements (TEs) within plant genomes. In plants, genome defense mechanisms employ various epigenetic modifications, such as DNA cytosine methylation, small RNAs, and histone protein modifications, to repress TEs. Notably, these repressive epigenetic modifications are typically absent from actively transcribed genes. Our primary objective is to unravel the mechanisms by which epigenetic processes differentiate between gene and TE sequences, how they precisely deposit specific chromatin modifications at their targets, and to comprehend their biological significance in terms of adaptation and genome evolution. Additionally, we aim to explore the influence of environmental signals on epigenome dynamics and phenotypic diversity in plants. Furthermore, we are actively engaged in collaborative research projects with the local Okinawan government, institutes, and industries, utilizing plant genomics approaches to address pressing issues in the Okinawan society.

1. Staff

  • Hidetoshi Saze, Associate Professor 
  • Matin Miryeganeh, Researcher (-May, 2022)
  • Leonardo Furci, Researcher
  • Jeremy Berthelier, Researcher
  • Atsushi Shimada, Staff scientist
  • Hiroki Tsutsui, Researcher (JSPS PD)
  • Kenji Osabe, Senior staff scientist
  • Oscar Juez Neira, Ph.D. Student
  • Munissa Sadykova, Ph.D. Student
  • Yoshiko Harukawa, Technical Staff
  • Yoko Fujitomi, Research Unit Administrator

2. Collaborations

2.1 Epigenetic regulation of immune response in Arabidopsis

  • Type of collaboration: Joint research
  • Researchers: Drs. Ken Shirasu and Shuta Asai, RIKEN Center for Sustainable Resource Science, Japan.

2.2 Epigenetic regulation of transposable elements in Arabidopsis

  • Type of collaboration: Joint research
  • Researcher: Dr. Hidetaka Ito, Faculty of Science, Hokkaido University, Japan

2.3 Okinawa Functional Rice project

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

3. Activities and Findings

Long-Read Sequencing Technology for Epigenome Analysis and Detection of Chimeric Gene-TE Transcripts in Arabidopsis

Understanding the prevalence and transcriptional regulation of transcripts originating from the interplay between transposable elements (TEs) and genes remains a significant knowledge gap in plant biology. To address this, we have leveraged the advancements in long-read sequencing technologies, which offer a comprehensive view of mRNA transcription and processing dynamics. Specifically, we employed Oxford Nanopore Direct RNA Sequencing (ONT-DRS) technology and developed a specialized bioinformatics pipeline called ParasiTE to investigate gene transcripts co-transcribed with TE sequences in the transcriptome of Arabidopsis thaliana (Berthelier et al., 2022). Additionally, we utilized nanopore DNA sequencing data to detect DNA methylation patterns within highly repetitive TE regions, which provides a valuable alternative to the limitations of short-read Bisulfite sequencing (BS-seq) analysis. Our investigation uncovered a widespread occurrence of chimeric TE-gene transcripts across thousands of gene loci in A. thaliana (Figure 1).

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Figure 1. (Left) Representative loci associated with TE-AS and TE-ATP events detected in DRS-AtRTD3. Red, TE annotation; Green, AtRTD3 annotation (collapsed); Blue, DRS-AtRTD3 annotation (extended). (Right) RNA processing events associated with ATE-G isoforms (TE-AS and TE-ATP). TE-AFE and TE-ALE are included in TE-ATSS and TE-ATTS, respectively. AS; Alternative Splicing, ATP; Alternative Transcript Production, IR; Intron Retention, ES; Exon Skipping, A5SS; Alternative 5′ Splicing Sites, A3SS; Alternative 3′ Splicing Sites, ATSS; Alternative Transcription Start Sites, ATTS; Alternative Transcription Termination Sites, AFE; Alternative First Exon, ALE; Alternative Last Exon. The number of TEs associated with ATE-G isoform events. Some TEs were included in several ATE-G isoform categories.The number of TEs associated with ATE-G isoform events. Figures are from Berthelier et al., 2022.   Notably, TE sequences often exhibit associations with alternative transcription start sites or transcription termination sites. Importantly, the epigenetic state of intragenic TEs influences RNA polymerase II (RNAPII) elongation and the utilization of alternative poly(A) signals within TE sequences, thereby regulating the production of alternative TE-gene isoforms (Figure 5C). The co-transcription and inclusion of TE-derived sequences in gene transcripts have substantial impacts on RNA stability and the environmental responses of specific loci. Thus, our study provides novel insights into the intricate TE-gene interactions that contribute to mRNA regulation, transcriptome diversity, and environmental responses in plants.  
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Figure 2. Representative genome loci showing TE-gene isoform production with TE-ATTS events. Tracks (from top to bottom): ChIP-seq data for RNA Pol II phosphorylated at Ser5/Ser2 in CTD repeats (bins per million); ChIP-seq data for IBM2 and EDM2 localization (bins per million); Col-0 ChIP-seq of H3K9me2 (reads per million); methylation levels of Col-0 in CG, CHG, and CHH contexts (0–100%); poly(A) sites obtained from the PlantAPA database; DRS read alignments of Col-0 and indicated mutants; TE and transcript annotations of AtRTD3 and DRS-AtRTD3 in this study and the orientation of genes and TEs.

4. Publications

4.1 Journals

  1. Berthelier J*, Furci L, Asai S, Sadykova M, Shimazaki M, Shirasu K, and Saze H* (2022). Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana. bioRxiv. https://doi.org/10.1101/2022.09.21.507229
  2. Nozawa K, Masuda S, Saze H, Ikeda Y, Suzuki T, Takagi H, Tanaka K, Ohama N, Niu X, Kato A, Ito H (2022). Epigenetic regulation of ecotype-specific expression of the heat-activated transposon ONSEN. Frontiers in Plant Science, 13: 899105.

4.2 Books and other one-time publications

  1. Furci L, Berthelier J, Juez O, Miryeganeh M, Saze H†. (2022). Chapter 15: “Plant Epigenomics”. Handbook of Epigenetics (Third Edition). p263-286. ELSEVIER. https://doi.org/10.1016/C2021-0-00437-5. (Book chapter)

4.3 Oral and Poster Presentations

  1. (Invited symposium presentation) Saze H. Epigenetic regulation of intragenic transposons and gene transcription in plant genomes. 2nd EPI-CATCH COST CA19125 Conference, Crete, Greece, Jul 14, 2022
  2. (Oral presentation) Fruci L, Young Scientist Meeting , Hiroshima, Japan, November 16-18, 2022
  3. (Oral presentation) Berthelier J, NIG seminar, National Institute of Genetics, Shizuoka, Oct. 5, 2022 (online)
  4. (Poster presentation) Berthelier J, CSHA, Awaji, Hyogo, Dec. 23-25
  5. (Oral presentation) Berthelier J, CNET conference, July 5, 2022
  6. (Poster presentation) Shimada A, Young Scientist Meeting , Hiroshima, Japan, November 16-18, 2022
  7. (Poster presentation) Juez O, CSHA, Awaji, Hyogo, Dec. 23-25
  8. (Poster presentation) Juez O, Mechanisms of Aging Conference, Cold Spring Harbor Laboratory, USA, September 27-October 1, 2022
  9. (Poster presentation) Juez O, CSHA, Awaji, Hyogo, Dec. 23-25
  10. (Poster presentation) Sadykova, Young Scientist Meeting , Hiroshima, Japan, November 16-18, 2022

5. Intellectual Property Rights and Other Specific Achievements

None

6. Meetings and Events

[Seminar]"Epigenetic aberrations to drive gastric tumorigenesis" by Prof. Atsushi Kaneda, Department of Molecular Oncology, Graduate School of Medicine, Chiba University, July 29, 2022

7. Other

Nothing to report.