Abstract
DNA methylation is an important epigenetic mark conserved in eukaryotes from fungi to animals and plants, where it plays a crucial role in regulating gene expression and transposon silencing. Once the methylation mark is established by de novo DNA methyltransferases, specific regulatory mechanisms are required to maintain the methylation state during chromatin replication, both during meiosis and mitosis. Plant DNA methylation is found in three contexts; CG, CHG, and CHH (H = A, T, C), which are established and maintained by a unique set of DNA methyltransferases and are regulated by plant-specific pathways. DNA methylation in plants is often associated with other epigenetic modifications, such as noncoding RNA and histone modifications. This chapter focuses on the structure, function, and regulatory mechanism of plant DNA methyltransferases and their crosstalk with other epigenetic pathways.
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Abbreviations
- 5mC:
-
5-Methyl-cytosine
- 6 mA:
-
6-Methyl-adenine
- AdoHcy:
-
S-Adenosyl-L-homocysteine
- AdoMet:
-
S-Adenosyl-L-methionine
- AGO4:
-
ARGONAUTE 4
- BAH domain:
-
Bromo-adjacent homology domain
- CMT:
-
CHROMOMETHYLASE
- DCL3:
-
DICER-LIKE 3
- DDM1:
-
DECREASED IN DNA METHYLATION 1
- DRM2:
-
DOMAINS REARRANGED METHYLTRANSFERASE 2
- ITC:
-
Isothermal titration calorimetry
- KYP:
-
KRYPTONITE
- MET1:
-
DNA METHYLTRANSFERASE 1
- MTase:
-
Methyltransferase
- PKMT:
-
Protein lysine methyltransferase
- Pol II/IV/V:
-
RNA polymerase II/IV/V
- RdDM:
-
RNA-directed DNA methylation
- RDR2:
-
RNA-DEPENDENT RNA POLYMERASE 2
- RFTD:
-
Replication foci targeting domain
- SET domain:
-
Su(var)3–9, enhancer of zeste, trithorax domain
- SHH1:
-
SAWADEE HOMEODOMAIN HOMOLOG 1
- SRA domain:
-
SET and RING finger-associated domain
- SUVH:
-
SUPPRESSOR OF VARIEGATION 3–9 HOMOLOG
- TE:
-
Transposable elements
- TRD:
-
Target recognition domain
- UBA:
-
Ubiquitin-associated domain
- UHRF1:
-
Ubiquitin-like PHD and RING finger domains 1
- VIM:
-
VARIANT IN METHYLATION
- ZMET2:
-
Zea methyltransferase 2
References
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M (2008) Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature 455(7214):818–821. https://doi.org/10.1038/nature07249
Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner C et al (2008) Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1. Nature 455(7214):822–825. https://doi.org/10.1038/nature07273
Bashtrykov P, Jankevicius G, Smarandache A, Jurkowska RZ, Ragozin S, Jeltsch A (2012) Specificity of Dnmt1 for methylation of hemimethylated CpG sites resides in its catalytic domain. Chem Biol 19(5):572–578. https://doi.org/10.1016/j.chembiol.2012.03.010
Bashtrykov P, Rajavelu A, Hackner B, Ragozin S, Carell T, Jeltsch A (2014) Targeted mutagenesis results in an activation of DNA methyltransferase 1 and confirms an autoinhibitory role of its RFTS domain. Chembiochem 15(5):743–748. https://doi.org/10.1002/cbic.201300740
Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 3(9):e3156. https://doi.org/10.1371/journal.pone.0003156
Bewick AJ, Ji L, Niederhuth CE, Willing EM, Hofmeister BT, Shi X et al (2016) On the origin and evolutionary consequences of gene body DNA methylation. Proc Natl Acad Sci U S A 113(32):9111–9116. https://doi.org/10.1073/pnas.1604666113
Bewick AJ, Niederhuth CE, Ji L, Rohr NA, Griffin PT, Leebens-Mack J et al (2017) The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. Genome Biol 18(1):65. https://doi.org/10.1186/s13059-017-1195-1
Blus BJ, Wiggins K, Khorasanizadeh S (2011) Epigenetic virtues of chromodomains. Crit Rev Biochem Mol Biol 46(6):507–526. https://doi.org/10.3109/10409238.2011.619164
Cao X, Jacobsen SE (2002a) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A 99(Suppl 4):16491–16498. https://doi.org/10.1073/pnas.162371599
Cao X, Jacobsen SE (2002b) Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12(13):1138–1144
Castel SE, Martienssen RA (2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 14(2):100–112. https://doi.org/10.1038/nrg3355
Chen J, Liu J, Jiang J, Qian S, Song J, Kabara R et al (2021) F-box protein CFK1 interacts with and degrades de novo DNA methyltransferase in Arabidopsis. New Phytol 229(6):3303–3317. https://doi.org/10.1111/nph.17103
Cheng X, Kumar S, Posfai J, Pflugrath JW, Roberts RJ (1993) Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell 74(2):299–307
Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H et al (2015) Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition. Plant J 83(6):1069–1081. https://doi.org/10.1111/tpj.12952
Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y et al (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466(7304):388–392. https://doi.org/10.1038/nature09147.
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD et al (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452(7184):215–219. https://doi.org/10.1038/nature06745
Dangwal M, Malik G, Kapoor S, Kapoor M (2013) De novo methyltransferase, OsDRM2, interacts with the ATP-dependent RNA helicase, OseIF4A, in rice. J Mol Biol 425(16):2853–2866. https://doi.org/10.1016/j.jmb.2013.05.021
Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, Caro E et al (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151(1):167–180. https://doi.org/10.1016/j.cell.2012.07.034
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S et al (2014) Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol Cell 55(3):495–504. https://doi.org/10.1016/j.molcel.2014.06.009
Du J, Johnson LM, Jacobsen SE, Patel DJ (2015) DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol 16(9):519–532. https://doi.org/10.1038/nrm4043
Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM et al (2021) Substrate deformation regulates DRM2-mediated DNA methylation in plants. Sci Adv 7(23). https://doi.org/10.1126/sciadv.abd9224
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR et al (2014) Pfam: the protein families database. Nucleic Acids Res 42(Database issue):D222–D230. https://doi.org/10.1093/nar/gkt1223
Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43(2–3):189–201
Fu Y, Luo GZ, Chen K, Deng X, Yu M, Han D et al (2015) N(6)-methyldeoxyadenosine marks active transcription start sites in chlamydomonas. Cell 161(4):879–892. https://doi.org/10.1016/j.cell.2015.04.010
Gallego-Bartolomé J, Liu W, Kuo PH, Feng S, Ghoshal B, Gardiner J et al (2019) Co-targeting RNA polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis. Cell 176(5):1068–82.e19. https://doi.org/10.1016/j.cell.2019.01.029
Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S et al (2020) Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Nat Commun 11(1):3355. https://doi.org/10.1038/s41467-020-17109-4
Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481–514. https://doi.org/10.1146/annurev.biochem.74.010904.153721
Gouil Q, Baulcombe DC (2016) DNA methylation signatures of the plant Chromomethyltransferases. PLoS Genet 12(12):e1006526. https://doi.org/10.1371/journal.pgen.1006526
Haag JR, Pikaard CS (2011) Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 12(8):483–492. https://doi.org/10.1038/nrm3152
Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, Pasa-Tolic L et al (2012) In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol Cell 48(5):811–818. https://doi.org/10.1016/j.molcel.2012.09.027
Haag JR, Brower-Toland B, Krieger EK, Sidorenko L, Nicora CD, Norbeck AD et al (2014) Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits. Cell Rep 9(1):378–390. https://doi.org/10.1016/j.celrep.2014.08.067
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008) The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455(7214):826–829. https://doi.org/10.1038/nature07280
He XJ, Ma ZY, Liu ZW (2014) Non-coding RNA transcription and RNA-directed DNA methylation in Arabidopsis. Mol Plant 7(9):1406–1414. https://doi.org/10.1093/mp/ssu075
He L, Zhao C, Zhang Q, Zinta G, Wang D, Lozano-Durán R et al (2021) Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability. Proc Natl Acad Sci U S A 118(35). https://doi.org/10.1073/pnas.2107320118
Henderson IR, Deleris A, Wong W, Zhong X, Chin HG, Horwitz GA et al (2010) The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet 6(10):e1001182. https://doi.org/10.1371/journal.pgen.1001182
Hu D, Yu Y, Wang C, Long Y, Liu Y, Feng L et al (2021) Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions. Plant Cell 33(9):2950–2964. https://doi.org/10.1093/plcell/koab162
Ishiyama S, Nishiyama A, Saeki Y, Moritsugu K, Morimoto D, Yamaguchi L et al (2017) Structure of the Dnmt1 reader module complexed with a unique two-mono-ubiquitin mark on histone H3 reveals the basis for DNA methylation maintenance. Mol Cell 68(2):350–60.e7. https://doi.org/10.1016/j.molcel.2017.09.037
Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416(6880):556–560. https://doi.org/10.1038/nature731
Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh PB et al (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112(6):308–315. https://doi.org/10.1007/s00412-004-0275-7
Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X (2007) Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449(7159):248–251. https://doi.org/10.1038/nature06146
Jiang J, Liu J, Sanders D, Qian S, Ren W, Song J et al (2021) UVR8 interacts with de novo DNA methyltransferase and suppresses DNA methylation in Arabidopsis. Nat Plants 7(2):184–197. https://doi.org/10.1038/s41477-020-00843-4
Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J et al (2007) The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17(4):379–384. https://doi.org/10.1016/j.cub.2007.01.009
Johnson LM, Law JA, Khattar A, Henderson IR, Jacobsen SE (2008) SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet 4(11):e1000280. https://doi.org/10.1371/journal.pgen.1000280
Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK et al (2014) SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature 507(7490):124–128. https://doi.org/10.1038/nature12931
Jurkowska RZ, Anspach N, Urbanke C, Jia D, Reinhardt R, Nellen W et al (2008) Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L. Nucleic Acids Res 36(21):6656–6663. https://doi.org/10.1093/nar/gkn747
Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA et al (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163(3):1109–1122
Kim MY, Zilberman D (2014) DNA methylation as a system of plant genomic immunity. Trends Plant Sci 19(5):320–326. https://doi.org/10.1016/j.tplants.2014.01.014
Kuo AJ, Song J, Cheung P, Ishibe-Murakami S, Yamazoe S, Chen JK et al (2012) The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome. Nature 484(7392):115–119. https://doi.org/10.1038/nature10956
Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11(3):204–220. https://doi.org/10.1038/nrg2719
Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, Wohlschlegel JA et al (2010) A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol 20(10):951–956. https://doi.org/10.1016/j.cub.2010.03.062
Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AM et al (2013) Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 498(7454):385–389. https://doi.org/10.1038/nature12178
Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B et al (2018) Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation. Proc Natl Acad Sci U S A 115(37):E8793–EE802. https://doi.org/10.1073/pnas.1809841115
Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S et al (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292(5524):2077–2080. https://doi.org/10.1126/science.1059745
Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH et al (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523–536. https://doi.org/10.1016/j.cell.2008.03.029
Liu ZW, Shao CR, Zhang CJ, Zhou JX, Zhang SW, Li L et al (2014) The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet 10(1):e1003948. https://doi.org/10.1371/journal.pgen.1003948
Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15(6):394–408. https://doi.org/10.1038/nrg3683
Niu Q, Song Z, Tang K, Chen L, Wang L, Ban T et al (2021) A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation. Nat Commun 12(1):3367. https://doi.org/10.1038/s41467-021-23637-4
Nozawa K, Chen J, Jiang J, Leichter SM, Yamada M, Suzuki T et al (2021) DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress. PLoS Genet 17(8):e1009710. https://doi.org/10.1371/journal.pgen.1009710
Patel DJ, Wang Z (2013) Readout of epigenetic modifications. Annu Rev Biochem 82:81–118. https://doi.org/10.1146/annurev-biochem-072711-165700
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D et al (2011) A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Genes Dev 25(2):137–152. https://doi.org/10.1101/gad.1980311
Rajakumara E, Nakarakanti NK, Nivya MA, Satish M (2016) Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain. Sci Rep 6:20161. https://doi.org/10.1038/srep20161
Ren W, Fan H, Grimm SA, Guo Y, Kim JJ, Yin J et al (2020) Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation. Proc Natl Acad Sci U S A 117(31):18439–18447. https://doi.org/10.1073/pnas.2009316117
Ren W, Fan H, Grimm SA, Kim JJ, Li L, Guo Y et al (2021) DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation. Nat Commun 12(1):2490. https://doi.org/10.1038/s41467-021-22665-4
Scheid R, Chen J, Zhong X (2021) Biological role and mechanism of chromatin readers in plants. Curr Opin Plant Biol 61:102008. https://doi.org/10.1016/j.pbi.2021.102008
Shen X, De Jonge J, Forsberg SK, Pettersson ME, Sheng Z, Hennig L et al (2014) Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genet 10(12):e1004842. https://doi.org/10.1371/journal.pgen.1004842
Song J, Rechkoblit O, Bestor TH, Patel DJ (2011) Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331(6020):1036–1040. https://doi.org/10.1126/science.1195380
Song J, Teplova M, Ishibe-Murakami S, Patel DJ (2012) Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science 335(6069):709–712. https://doi.org/10.1126/science.1214453
Stoddard CI, Feng S, Campbell MG, Liu W, Wang H, Zhong X et al (2019) A nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase. Mol Cell 73(1):73–83.e6. https://doi.org/10.1016/j.molcel.2018.10.006
Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152(1–2):352–364. https://doi.org/10.1016/j.cell.2012.10.054
Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L et al (2014) Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol 21(1):64–72. https://doi.org/10.1038/nsmb.2735
Syeda F, Fagan RL, Wean M, Avvakumov GV, Walker JR, Xue S et al (2011) The replication focus targeting sequence (RFTS) domain is a DNA-competitive inhibitor of Dnmt1. J Biol Chem 286(17):15344–15351. https://doi.org/10.1074/jbc.M110.209882
Takeshita K, Suetake I, Yamashita E, Suga M, Narita H, Nakagawa A et al (2011) Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1). Proc Natl Acad Sci U S A 108(22):9055–9059. https://doi.org/10.1073/pnas.1019629108
Vaniushin BF, Kadyrova D, Karimov K, Belozerskii AN (1971) Minor bases in DNA of higher plants. Biokhimiia 36(6):1251–1258
Vanyushin BF, Ashapkin VV (2011) DNA methylation in higher plants: past, present and future. Biochim Biophys Acta 1809(8):360–368. https://doi.org/10.1016/j.bbagrm.2011.04.006
Wang Q, Xue Y, Zhang L, Zhong Z, Feng S, Wang C et al (2021a) Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Science 374(6571):1152–1157. https://doi.org/10.1126/science.abl4546
Wang Y, Zhou X, Luo J, Lv S, Liu R, Du X et al (2021b) Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2. J Integr Plant Biol 63(6):1091–1096. https://doi.org/10.1111/jipb.13103
Wendte JM, Schmitz RJ (2018) Specifications of targeting heterochromatin modifications in plants. Mol Plant 11(3):381–387. https://doi.org/10.1016/j.molp.2017.10.002
Wendte JM, Zhang Y, Ji L, Shi X, Hazarika RR, Shahryary Y et al (2019) Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. elife 8:e47891. https://doi.org/10.7554/eLife.47891
Woo HR, Dittmer TA, Richards EJ (2008) Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. PLoS Genet 4(8):e1000156. https://doi.org/10.1371/journal.pgen.1000156
Yaari R, Noy-Malka C, Wiedemann G, Auerbach Gershovitz N, Reski R, Katz A et al (2015) DNA METHYLTRANSFERASE 1 is involved in (m)CG and (m)CCG DNA methylation and is essential for sporophyte development in Physcomitrella patens. Plant Mol Biol 88(4–5):387–400. https://doi.org/10.1007/s11103-015-0328-8
Yang N, Xu RM (2013) Structure and function of the BAH domain in chromatin biology. Crit Rev Biochem Mol Biol 48(3):211–221. https://doi.org/10.3109/10409238.2012.742035
Zabet NR, Catoni M, Prischi F, Paszkowski J (2017) Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. Nucleic Acids Res 45(7):3777–3784. https://doi.org/10.1093/nar/gkw1330
Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K et al (2013) The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153(1):193–205. https://doi.org/10.1016/j.cell.2013.02.033
Zhai J, Bischof S, Wang H, Feng S, Lee TF, Teng C et al (2015) A one precursor one siRNA model for pol IV-dependent siRNA biogenesis. Cell 163(2):445–455. https://doi.org/10.1016/j.cell.2015.09.032
Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J et al (2013) DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci U S A 110(20):8290–8295. https://doi.org/10.1073/pnas.1300585110
Zhang H, Lang Z, Zhu JK (2018a) Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol 19(8):489–506. https://doi.org/10.1038/s41580-018-0016-z
Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L et al (2018b) Structural basis for DNMT3A-mediated de novo DNA methylation. Nature 554(7692):387–391. https://doi.org/10.1038/nature25477
Zhao Y, Chen X (2014) Noncoding RNAs and DNA methylation in plants. Natl Sci Rev 1(2):219–229. https://doi.org/10.1093/nsr/nwu003
Zhong X, Du J, Hale CJ, Gallego-Bartolome J, Feng S, Vashisht AA et al (2014) Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell 157(5):1050–1060. https://doi.org/10.1016/j.cell.2014.03.056
Zhong X, Hale CJ, Nguyen M, Ausin I, Groth M, Hetzel J et al (2015) Domains rearranged methyltransferase3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis. Proc Natl Acad Sci U S A 112(3):911–916. https://doi.org/10.1073/pnas.1423603112
Acknowledgments
We apologize to those whose work was not discussed due to the space limitation. We would like to thank Zhong lab members Dr. Jianjun Jiang and Ray Scheid for the critical reading of this manuscript. This work was supported by NSF (MCB-1552455 and MCB-2043544) and the NIH-MIRA (R35GM124806) awards to XZ, and the Shenzhen Science and Technology Program (JCYJ20200109110403829) to JD.
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Leichter, S.M., Du, J., Zhong, X. (2022). Structure and Mechanism of Plant DNA Methyltransferases. In: Jeltsch, A., Jurkowska, R.Z. (eds) DNA Methyltransferases - Role and Function. Advances in Experimental Medicine and Biology, vol 1389. Springer, Cham. https://doi.org/10.1007/978-3-031-11454-0_6
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