Decrease in DNA Methylation I (DDM1)

DDM1, Decreased DNA Methylation I, is a plant gene that encodes a nucleosome remodeler which facilitates DNA methylation. The DDM1 gene has been described extensively in Arabidopsis thaliana and also in maize. The protein has been described to be similar to the SWI2/SNF2 chromatin remodeling proteins.[1]

Since DNA methylation occurs mostly in transposable elements (TE),[2] DDM1 is thought to be a crucial function in silencing TEs.

Arabidopsis thaliana (A. thaliana)

DDM1 is required for DNA methylation in highly heterochromatin transposable elements.[3] DDM1, therefore, often silences transposable elements but the mutation in Arabidopsis thaliana is not embryo lethal.[3] DDM1 mutants have also been described to be an epigenetic link between salicylic acid production and heterosis.[4] A. thaliana has a single copy of the DDM1 gene.

Maize

DDM1 is being further explored in maize. Unlike A. thaliana, maize has two copies of the gene: CHR101 and CHR106.[5] In maize, the double mutant of DDM1 is embryo lethal. However, other studies are using the heterozygote mutant. The maize genome is 80% transposons[6] so DDM1 function is quite important.

References
  1. Cho, Eun Ju; Choi, Seung Hee; Kim, Ji Hong; Kim, Ji Eun; Lee, Min Hee; Chung, Byung Yeoup; Woo, Hye Ryun; Kim, Jin-Hong; Candela, Hector (11 January 2016). "A Mutation in Plant-Specific SWI2/SNF2-Like Chromatin-Remodeling Proteins, DRD1 and DDM1, Delays Leaf Senescence in Arabidopsis thaliana". PLOS ONE. 11 (1): e0146826. doi:10.1371/journal.pone.0146826. PMC 4709239. PMID 26752684.
  2. Law, Julie A.; Jacobsen, Steven E. (March 2010). "Establishing, maintaining and modifying DNA methylation patterns in plants and animals". Nature Reviews Genetics. 11 (3): 204–220. doi:10.1038/nrg2719. ISSN 1471-0056. PMC 3034103. PMID 20142834.
  3. Zemach, Assaf; Kim, M. Yvonne; Hsieh, Ping-Hung; Coleman-Derr, Devin; Eshed-Williams, Leor; Thao, Ka; Harmer, Stacey L.; Zilberman, Daniel (March 2013). "The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin". Cell. 153 (1): 193–205. doi:10.1016/j.cell.2013.02.033. PMC 4035305. PMID 23540698.
  4. Zhang, Qingzhu; Li, Yanqiang; Xu, Tao; Srivastava, Ashish Kumar; Wang, Dong; Zeng, Liang; Yang, Lan; He, Li; Zhang, Heng (December 2016). "The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism". Cell Discovery. 2 (1): 16027. doi:10.1038/celldisc.2016.27. ISSN 2056-5968. PMC 4977722. PMID 27551435.
  5. Li, Qing; Eichten, Steven R.; Hermanson, Peter J.; Zaunbrecher, Virginia M.; Song, Jawon; Wendt, Jennifer; Rosenbaum, Heidi; Madzima, Thelma F.; Sloan, Amy E. (December 2014). "Genetic Perturbation of the Maize Methylome". The Plant Cell. 26 (12): 4602–4616. doi:10.1105/tpc.114.133140. ISSN 1040-4651. PMC 4311211. PMID 25527708.
  6. Schnable, P. S.; Ware, D.; Fulton, R. S.; Stein, J. C.; Wei, F.; Pasternak, S.; Liang, C.; Zhang, J.; Fulton, L. (2009-11-20). "The B73 Maize Genome: Complexity, Diversity, and Dynamics". Science. 326 (5956): 1112–1115. doi:10.1126/science.1178534. ISSN 0036-8075. PMID 19965430.
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