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Items: 1 to 20 of 21

1.
Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1
Akihisa Osakabe, Yoshimasa Takizawa, Naoki Horikoshi, Suguru Hatazawa, Lumi Negishi, Shoko Sato, Frédéric Berger, Tetsuji Kakutani, Hitoshi Kurumizaka
Nat Commun. 2024; 15: 5187. Published online 2024 Jul 11. doi: 10.1038/s41467-024-49465-w
PMCID:
PMC11239853
AbstractArticlePDF–10M
2.
Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation
Seung Cho Lee, Dexter W. Adams, Jonathan J. Ipsaro, Jonathan Cahn, Jason Lynn, Hyun-Soo Kim, Benjamin Berube, Viktoria Major, Joseph P. Calarco, Chantal LeBlanc, Sonali Bhattacharjee, Umamaheswari Ramu, Daniel Grimanelli, Yannick Jacob, Philipp Voigt, Leemor Joshua-Tor, Robert A. Martienssen
Cell. Author manuscript; available in PMC 2023 Nov 28.
Published in final edited form as: Cell. 2023 Sep 14; 186(19): 4100–4116.e15. Published online 2023 Aug 28. doi: 10.1016/j.cell.2023.08.001
PMCID:
PMC10529913
AbstractArticlePDF–3.6M
3.
DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis
Jincong Zhou, Xue Lei, Sarfraz Shafiq, Weifeng Zhang, Qin Li, Kuan Li, Jiafu Zhu, Zhicheng Dong, Xin-jian He, Qianwen Sun
Sci Adv. 2023 Aug; 9(32): eadg2699. Published online 2023 Aug 11. doi: 10.1126/sciadv.adg2699
PMCID:
PMC10421056
AbstractArticlePDF–1.6M
4.
DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis
Seungchul Lee, Jaemyung Choi, Jihwan Park, Chang Pyo Hong, Daeseok Choi, Soeun Han, Kyuha Choi, Tae-Young Roh, Daehee Hwang, Ildoo Hwang
Genome Biol. 2023; 24: 106. Published online 2023 May 5. doi: 10.1186/s13059-023-02952-7
PMCID:
PMC10161647
AbstractArticlePDF–3.6M
5.
Mutation in DDM1 inhibits the homology directed repair of double strand breaks
Seung Hee Choi, Tae Ho Ryu, Jeong-Il Kim, Sungbeom Lee, Seung Sik Lee, Jin-Hong Kim
PLoS One. 2019; 14(2): e0211878. Published online 2019 Feb 11. doi: 10.1371/journal.pone.0211878
PMCID:
PMC6370192
AbstractArticlePDF–2.8M
6.
DDM1 guards against telomere truncation in Arabidopsis
Xiaoyuan Xie, Dorothy E. Shippen
Plant Cell Rep. Author manuscript; available in PMC 2018 Apr 2.
Published in final edited form as: Plant Cell Rep. 2018 Mar; 37(3): 501–513. Published online 2018 Feb 1. doi: 10.1007/s00299-017-2245-6
PMCID:
PMC5880217
AbstractArticlePDF–665K
7.
DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
David B Lyons, Daniel Zilberman
eLife. 2017; 6: e30674. Published online 2017 Nov 15. doi: 10.7554/eLife.30674
PMCID:
PMC5728721
AbstractArticlePDF–1.5M
8.
CrY2H-seq: a massively-multiplexed assay for deep coverage interactome mapping
Shelly A. Wanamaker, Renee M. Garza, Andrew MacWilliams, Joseph R. Nery, Anna Bartlett, Rosa Castanon, Adeline Goubil, Joseph Feeney, Ronan O’Malley, Shao-shan Carol Huang, Zhuzhu Z. Zhang, Mary Galli, Joseph R. Ecker
Nat Methods. Author manuscript; available in PMC 2017 Dec 26.
Published in final edited form as: Nat Methods. 2017 Aug; 14(8): 819–825. Published online 2017 Jun 26. doi: 10.1038/nmeth.4343
Correction in:
Nat Methods. 2023 Jan 23
PMCID:
PMC5564216
AbstractArticlePDF–1.3M
9.
Role of DNA methylation in hybrid vigor in Arabidopsis thaliana
Takahiro Kawanabe, Sonoko Ishikura, Naomi Miyaji, Taku Sasaki, Li Min Wu, Etsuko Itabashi, Satoko Takada, Motoki Shimizu, Takeshi Takasaki-Yasuda, Kenji Osabe, W. James Peacock, Elizabeth S. Dennis, Ryo Fujimoto
Proc Natl Acad Sci U S A. 2016 Oct 25; 113(43): E6704–E6711. Published online 2016 Oct 7. doi: 10.1073/pnas.1613372113
PMCID:
PMC5087013
AbstractArticlePDF–1.5M
10.
A Mutation in Plant-Specific SWI2/SNF2-Like Chromatin-Remodeling Proteins, DRD1 and DDM1, Delays Leaf Senescence in Arabidopsis thaliana
Eun Ju Cho, Seung Hee Choi, Ji Hong Kim, Ji Eun Kim, Min Hee Lee, Byung Yeoup Chung, Hye Ryun Woo, Jin-Hong Kim
PLoS One. 2016; 11(1): e0146826. Published online 2016 Jan 11. doi: 10.1371/journal.pone.0146826
PMCID:
PMC4709239
AbstractArticlePDF–7.1M
11.
Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis
Tasuku Ito, Yoshiaki Tarutani, Taiko Kim To, Mohamed Kassam, Evelyne Duvernois-Berthet, Sandra Cortijo, Kazuya Takashima, Hidetoshi Saze, Atsushi Toyoda, Asao Fujiyama, Vincent Colot, Tetsuji Kakutani
PLoS Genet. 2015 Apr; 11(4): e1005154. Published online 2015 Apr 22. doi: 10.1371/journal.pgen.1005154
PMCID:
PMC4406451
AbstractArticlePDF–2.5M
12.
Identification of genes preventing transgenerational transmission of stress-induced epigenetic states
Mayumi Iwasaki, Jerzy Paszkowski
Proc Natl Acad Sci U S A. 2014 Jun 10; 111(23): 8547–8552. Published online 2014 May 27. doi: 10.1073/pnas.1402275111
PMCID:
PMC4060648
AbstractArticlePDF–1.3M
13.
The nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin
Assaf Zemach, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, Daniel Zilberman
Cell. Author manuscript; available in PMC 2014 May 27.
Published in final edited form as: Cell. 2013 Mar 28; 153(1): 193–205. doi: 10.1016/j.cell.2013.02.033
PMCID:
PMC4035305
AbstractArticlePDF–3.2M
14.
Deficiency in DNA methylation increases meiotic crossover rates in euchromatic but not in heterochromatic regions in Arabidopsis
Cathy Melamed-Bessudo, Avraham A. Levy
Proc Natl Acad Sci U S A. 2012 Apr 17; 109(16): E981–E988. Published online 2012 Mar 28. doi: 10.1073/pnas.1120742109
PMCID:
PMC3341010
AbstractArticlePDF–848K
15.
Heterochromatic siRNAs and DDM1 Independently Silence Aberrant 5S rDNA Transcripts in Arabidopsis
Todd Blevins, Olga Pontes, Craig S. Pikaard, Frederick Meins, Jr
PLoS One. 2009; 4(6): e5932. Published online 2009 Jun 16. doi: 10.1371/journal.pone.0005932
PMCID:
PMC2691480
AbstractArticlePDF–2.0M
16.
RNAi-mediated gene silencing reveals involvement of Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation
Yan Ma Crane, Stanton B. Gelvin
Proc Natl Acad Sci U S A. 2007 Sep 18; 104(38): 15156–15161. Published online 2007 Sep 7. doi: 10.1073/pnas.0706986104
PMCID:
PMC1986629
AbstractArticlePDF–866K
17.
Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1
Hidetoshi Saze, Tetsuji Kakutani
EMBO J. 2007 Aug 8; 26(15): 3641–3652. Published online 2007 Jul 12. doi: 10.1038/sj.emboj.7601788
PMCID:
PMC1949009
AbstractArticlePDF–337K
18.
Regulation of Seed Size by Hypomethylation of Maternal and Paternal Genomes
Wenyan Xiao, Roy C. Brown, Betty E. Lemmon, John J. Harada, Robert B. Goldberg, Robert L. Fischer
Plant Physiol. 2006 Nov; 142(3): 1160–1168. doi: 10.1104/pp.106.088849
PMCID:
PMC1630758
AbstractArticlePDF–506K
19.
DDM1 Binds Arabidopsis Methyl-CpG Binding Domain Proteins and Affects Their Subnuclear Localization
Assaf Zemach, Yan Li, Bess Wayburn, Hagit Ben-Meir, Vladimir Kiss, Yigal Avivi, Vyacheslav Kalchenko, Steven E. Jacobsen, Gideon Grafi
Plant Cell. 2005 May; 17(5): 1549–1558. doi: 10.1105/tpc.105.031567
PMCID:
PMC1091773
AbstractArticlePDF–342K
20.
The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis
Jeffrey A. Jeddeloh, Judith Bender, Eric J. Richards
Genes Dev. 1998 Jun 1; 12(11): 1714–1725. doi: 10.1101/gad.12.11.1714
PMCID:
PMC316876
AbstractArticlePDF–421K

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