Peer-reviewed primary publications (†corresponding author)
Furci L†, Berthelier J, Saze H. (2024). RNA N6-adenine methylation dynamics impact Hyaloperonospora arabidopsidis resistance in Arabidopsis. Plant Physiol. 2024 Jul 11: kiae373. doi: 10.1093/plphys/kiae373.
Takei T, Tsukada M, Tamura K, Hara-Nishimura I, Fukao Y, Kurihara Y, Matsui M, Saze H, Tsuzuki M, Watanabe Y, Hamada T. (2024). ARGONAUTE1-binding Tudor domain proteins function in small interfering RNA production for RNA-directed DNA methylation. Plant Physiol. 2024 May 31;195(2):1333-1346. doi: 10.1093/plphys/kiae135.
Chavan S, Saze H, Tanaka F. (2023) Chemical Modification of Peptides and Proteins Using Spirooxindole Oxirane Derivatives. Adv. Synth. Catal. 2023. July 4; 363(13): 2171-2176. doi: doi.org/ 10.1002/ adsc.202300578.
Berthelier J†, Furci L, Asai S, Sadykova M, Shimazaki T, Shirasu K, Saze H†. (2023) Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana. Nat Commun. Jun 5;14(1):3248. doi: 10.1038/s41467-023-38954-z.
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. Front Plant Sci. 2022 Jul 18;13:899105. doi: 10.3389/fpls.2022.899105. eCollection 2022.
Miryeganeh M†, Marlétaz F, Gavriouchkina D, Saze H†. (2022) 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.
Miryeganeh M†, Saze H. (2021) 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.
Miryeganeh M†, Saze H. (2021) 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.
Irei A, Miryeganeh M, Tamashiro M, Saze H, Urasaki N, Tarora K. (2021). Development of a male specific genetic marker for Garcinia subelliptica Merr. tree. J For Res. 1-8. https://doi.org/10.1080/13416979.2021.1897060.
Le NT, Harukawa Y, Miura S, Boer D, Kawabe A, Saze H.† (2020) Epigenetic regulation of spurious transcription initiation in Arabidopsis. Nat Commun. Jun 26;11(1):3224. doi: 10.1038/s41467-020-16951-w.
Araki S, Le NT, Koizumi K, Villar-Briones A, Nonomura KI, Endo M, Inoue H, Saze H, Komiya R. (2020). miR2118-dependent U-rich phasiRNA production in rice anther wall development. Nat Commun. Jun 19;11(1):3115. doi: 10.1038/s41467-020-16637-3.
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
Osabe K, Harukawa Y, Miura S, Saze H.† (2017). Epigenetic Regulation of Intronic Transgenes in Arabidopsis. Sci Rep. Mar 24;7:45166. doi: 10.1038/srep45166.
Ito H, Kim JM, Matsunaga W, Saze H, Matsui A, Endo TA, Harukawa Y, Takagi H, Yaegashi H, Masuta Y, Masuda S, Ishida J, Tanaka M, Takahashi S, Morosawa T, Toyoda T, Kakutani T, Kato A, Seki M. (2016). A Stress-Activated Transposon in Arabidopsis Induces Transgenerational Abscisic Acid Insensitivity. Sci Rep. 6:23181. doi: 10.1038/srep23181.
Ito T, Tarutani Y, To TK, Kassam M, Duvernois-Berthet E, Cortijo S, Takashima K, Saze H, Toyoda A, Fujiyama A, Colot V, Kakutani T. (2015). Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis. PLoS Genet. 11(4):e1005154.
Le Tu N., Miyazaki Y., Takuno S., Saze H.† (2015). Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana. Nucleic Acids Res., doi: 10.1093/nar/gkv258
Saze H.†, Kitayama J, Takashima K, Miura S, Harukawa Y, Ito T, Kakutani T. (2013). Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin.Nat Commun., 4:2301.
Sasaki T, Kobayashi A, Saze H, Kakutani T. (2012) RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of a chromatin remodeling gene DDM1. Plant J., 70(5): 750-758.
Inagaki S, Miura-Kamio A, Nakamura Y, Lu F, Cui X, Cao X, Kimura H, Saze H, Kakutani T. (2010). Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO J., 29(20):3496-506.
Miura, A., Nakamura, M., Inagaki, S., Kobayashi, A., Saze, H., and Kakutani, T. (2009). An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J., 28, 1078-1086.
Saze, H.†, Shiraishi, A., Miura, A., and Kakutani, T. (2008).Control of genic DNA methylation by a jmjC-domain containing protein in Arabidopsis thaliana. Science, 319, 462-465.
Saze, H.†, and Kakutani, T. (2007). Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J.,26, 3641-3652.
Kinoshita, Y., Saze, H., Kinoshita, T., Miura, A., Soppe, W., Koornneef, M., and Kakutani, T. (2007). Control of FWA gene silencing in Arabidopsis thaliana by SINE-related dirct repeats.Plant J., 49, 38-45.
Tariq, M., Saze, H., Probst, A., Lichota, J., Habu, Y., and Paszkowski, J. (2003). Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc. Natl. Acad. Sci. USA, 100, 8823-8827.
Saze, H.†, Mittelsten-Scheid, O., and Paszkowski, J. (2003). Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis.Nat Genet., 34, 65-69.
Saze, H., Ueno, Y., Hisabori, T., Hayashi, H., and Izui, K. (2001). Thioredoxin-mediated reductive activation of a protein kinase for the regulatory phosphorylation of C4-form Phosphoenolpyruvate Carboxylase from Maize. Plant Cell Physiol., 42, 1295-1302.
Other Publications
(Editorial) Saze H, Springer N. (2023). Editorial overview: Delving into organizational principles of plant genomes. Curr Opin Plant Biol. Oct 11:76:102458. doi: 10.1016/j.pbi.2023.102458.
(Book chapter) 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)
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.
(Review) Miryeganeh M†, Saze H†. (2020). Epigenetic inheritance and plant evolution. Population Ecology 62 (1), 17-27
(Review) Saze H. (2018). Epigenetic regulation of intragenic transposable elements: a two-edged sword
J Biochem. 164 (5), 323-328
(Review) Espinas NA†, Saze H, Saijo Y.† (2016). Epigenetic Control of Defense Signaling and Priming in Plants. Front Plant Sci. 2016 Aug 11;7:1201. doi: 10.3389/fpls.2016.01201.
(Review) To TK, Saze H, Kakutani T. (2015). DNA Methylation within Transcribed Regions. Plant Physiol., 168(4):1219-25. doi: 10.1104/pp.15.00543. Epub 2015 Jul 4.
(Review) Saze, H.† (2012).Transgenerational Inheritance of Induced Changes in the Epigenetic State of Chromatin in Plants. Genes Genet Systems, 87(3): 145-52.
(Review) Saze, H, Tsugane K, Kanno T and Nishimura T. (2012). DNA Methylation in Plants: Relationship with Small RNAs and Histone Modifications, and Functions in Transposon Inactivation. Plant Cell Physiol., 53(5): 766-84.
(Review) Saze, H and Kakutani T. (2011) Differentiation of epigenetic modifications between transposons and genes. Curr Opin Plant Biol., 14(1):81-7.
(Review) Saze, H.† (2008). Epigenetic Memory Transmission through Mitosis and Meiosis in Plants. Semin. Cell Dev. Biol. 19, 527-536.
(Review) Saze, H.†, Sasaki, T., and Kakutani, T. (2008). Negative Regulation of DNA Methylation in Plants. Epigenetics 3,122-124.