Finnegan EJ, Genger RK, Kovac K, Peacock WJ, Dennis ES. DNA methylation and the promotion of flowering by vernalization. Proc Natl Acad Sci U S A. 1998;95(10):5824–9.
Article CAS PubMed PubMed Central Google Scholar
Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010;11(3):204–20.
Article CAS PubMed PubMed Central Google Scholar
Cao X, Jacobsen SE. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol. 2002;12(13):1138–44.
Article CAS PubMed Google Scholar
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 2006;126(6):1189–201.
Article CAS PubMed Google Scholar
Zhang H, Zhu JK. Active DNA demethylation in plants and animals. Cold Spring Harb Symp Quant Biol. 2012;77:161–73.
Article CAS PubMed PubMed Central Google Scholar
Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, et al. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res. 2013;23(4):628–37.
Article CAS PubMed PubMed Central Google Scholar
Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, et al. RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc Natl Acad Sci U S A. 2015;112(47):14728–33.
Article CAS PubMed PubMed Central Google Scholar
Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, et al. Intragenic DNA methylation prevents spurious transcription initiation. Nature. 2017;543(7643):72–7.
Article CAS PubMed Google Scholar
Schmitz RJ, Lewis ZA, Goll MG. DNA methylation: shared and divergent features across eukaryotes. Trends Genet. 2019;35(11):818–27.
Article CAS PubMed PubMed Central Google Scholar
Muyle AM, Ross-Ibarra J, Seymour DK, Gaut BS. Gene body methylation is under selection in Arabidopsis thaliana. Genetics. 2021;218(2):iyab061.
Article PubMed PubMed Central Google Scholar
Muyle AM, Seymour DK, Lv Y, Huettel B, Gaut BS. Gene body methylation in plants: mechanisms, functions, and important implications for understanding evolutionary processes. Genome Biol Evol. 2022;14(4):evac038.
Article CAS PubMed PubMed Central Google Scholar
Williams CJ, Dai D, Tran KA, Monroe JG, Williams BP. Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants. Genome Biol. 2023;24(1):227.
Article CAS PubMed PubMed Central Google Scholar
Ai P, Xue J, Shi Z, Liu Y, Li Z, Li T, et al. Genome-wide characterization and expression analysis of MYB transcription factors in Chrysanthemum nankingense. BMC Plant Biol. 2023;23(1):140.
Article CAS PubMed PubMed Central Google Scholar
Lee S, Choi J, Park J, Hong CP, Choi D, Han S, et al. DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis. Genome Biol. 2023;24(1):106.
Article CAS PubMed PubMed Central Google Scholar
Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AM, et al. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature. 2013;498(7454):385–9.
Article CAS PubMed PubMed Central Google Scholar
Zhou M, Palanca AMS, Law JA. Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family. Nat Genet. 2018;50(6):865–73.
Article CAS PubMed PubMed Central Google Scholar
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, et al. Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science. 2021;374(6575):1579–86.
Article CAS PubMed Google Scholar
Singh J, Mishra V, Wang F, Huang HY, Pikaard CS. Reaction mechanisms of Pol IV, RDR2, and DCL3 drive RNA channeling in the siRNA-directed DNA methylation pathway. Mol Cell. 2019;75(3):576–89.
Article CAS PubMed PubMed Central Google Scholar
He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, et al. An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell. 2009;137(3):498–508.
Article CAS PubMed PubMed Central Google Scholar
Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet. 2009;41(5):630–4.
Article CAS PubMed PubMed Central Google Scholar
Matzke MA, Mosher RA. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet. 2014;15(6):394–408.
Article CAS PubMed Google Scholar
Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJ, Matzke M. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. Embo J. 2006;25(12):2828–36.
Article CAS PubMed PubMed Central Google Scholar
Jeddeloh JA, Stokes TL, Richards EJ. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet. 1999;22(1):94–7.
Article CAS PubMed Google Scholar
Jones L, Ratcliff F, Baulcombe DC. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr Biol. 2001;11(10):747–57.
Article CAS PubMed Google Scholar
Liu ZW, Shao CR, Zhang CJ, Zhou JX, Zhang SW, Li L, et al. The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet. 2014;10(1): e1003948.
Article PubMed PubMed Central Google Scholar
Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol. 2014;21(1):64–72.
Article CAS PubMed Google Scholar
Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153(1):193–205.
Article CAS PubMed PubMed Central Google Scholar
Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell. 2002;110(1):33–42.
Comments (0)