Publications

Selected Publications

  • Tsukahara S, Bousios A, Perez-Roman E, Yamaguchi S, Leduque B, Nakano A, Naish M, Osakabe A, Toyoda A, Ito H, Edera A, Tominaga S, Juliarni, Kato K, Oda S, Inagaki S, Lorković Z, Nagaki K, Berger F, Kawabe A, Quadrana L, Henderson I, Kakutani T (2025) Centrophilic retrotransposon integration via CENH3 chromatin in Arabidopsis. Nature online Pubmed
  • Mori S, Oya S, Takahashi M, Takashima K, Inagaki S, Kakutani T (2023) Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in Arabidopsis. EMBO J 42, e113798. Pubmed
  • Oya S, Takahashi M, Takashima K, Kakutani T, Inagaki S (2022) Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation. Nature Commun 13, 4521. Pubmed
  • To TK, Yamasaki C, Oda S, Tominaga S, Kobayashi A, Tarutani Y, Kakutani T (2022) Local and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis. Nature Commun 13, 861. Pubmed
  • Inagaki S, Takahashi M, Takashima K, Oya S, Kakutani T (2021) Chromatin-based mechanisms to coordinate convergent overlapping transcription. Nature Plants 7, 295-302. Pubmed
  • To TK, Nishizawa Y, Inagaki S, Tarutani Y, Tominaga S, Toyoda A, Fujiyama A, Berger F, Kakutani T. (2020) RNA interference-independent reprogramming of DNA methylation in Arabidopsis. Nature Plants 6, 1455-1467. Pubmed
  • Hosaka A, Saito R, Takashima K, Sasaki T, Fu Y, Kawabe A, Ito T, Toyoda A, Fujiyama A, Tarutani Y, Kakutani T. (2017) Evolution of sequence-specific anti-silencing systems in Arabidopsis. Nature Commun 8, 2161. Pubmed
  • Inagaki S, Takahashi M, Hosaka A, Ito T, Toyoda A, Fujiyama A, Tarutani Y, Kakutani T (2017) Gene-body chromatin modification dynamics mediate epigenome differentiation in Arabidopsis. EMBO J  36, 970-980. Pubmed
  • Fu Y, Kawabe A, Etcheverry M, Ito T, Toyoda A, Fujiyama A, Colot V, Tarutani Y, Kakutani T (2013) Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor. EMBO J 32, 2407-17. Pubmed
  • 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. Nature Commun 4, 2301. Pubmed
  • Tsukahara S, Kawabe A, Kobayashi A, Ito T, Aizu T, Shin-i T, Toyoda A, Fujiyama A, Tarutani Y, Kakutani T (2012) Centromere-targeted de novo integration of an LTR retrotransposon of Arabidopdid lyrata. Genes Dev 26, 705-13. Pubmed
  • 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, 3496-506. Pubmed
  • Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, and Kakutani T (2009) Bursts of retrotransposition reproduced in Arabidopsis.  Nature 303, 423-6. Pubmed
  • Miura A, Nakmura 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, 1078-86. Pubmed
  • 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, 462-5. Pubmed
  • Saze H, and Kakutani T (2007) Heritable epigenetic mutation of a transposon-flanked gene due to lack of the chromatin-remodeling factor DDM1.  EMBO J 26, 3641-52. Pubmed
  • Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Fischer RL, and Kakutani T (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303, 521-3. Pubmed
  • Miura, A., Yonebayashi, S., Watanabe, K., Toyama, T., Shimada, H., Kakutani, T. (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411, 212-4. Pubmed