Mechanistic Basis for Maintenance of CHG DNA Methylation in Plants

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

[20] Processing of X-ray diffraction data collected in oscillation mode

Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475 · see citing works

<i>Coot</i> : model-building tools for molecular graphics

Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works

fastp: an ultra-fast all-in-one FASTQ preprocessor

(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works

<i>Phaser</i> crystallographic software

McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612 · see citing works

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works

The language of covalent histone modifications

Strahl, B. D., & Allis, C. D. (2000) · Nature · doi:10.1038/47412 · Cited by 8,679 · see citing works

DNA methylation patterns and epigenetic memory

Bird, A. (2002) · Genes &amp; Development · doi:10.1101/gad.947102 · Cited by 7,124 · see citing works

Human DNA methylomes at base resolution show widespread epigenomic differences

Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673 · see citing works

<i>PHENIX</i> : building new software for automated crystallographic structure determination

Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902016657 · Cited by 4,361 · see citing works

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

Law, J. A., & Jacobsen, S. E. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2719 · Cited by 3,868 · see citing works

deepTools: a flexible platform for exploring deep-sequencing data

Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A., & Manke, T. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku365 · Cited by 3,738 · see citing works

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

Cokus, S. J., Feng, S.-H., Zhang, X.-Y., Chen, Z., Merriman, B., Haudenschild, C., Pradhan, S., Nelson, S., Pellegrini, M., & Jacobsen, S. (2008) · Nature · doi:10.1038/nature06745 · Cited by 2,278 · see citing works

Linking DNA methylation and histone modification: patterns and paradigms

Cedar, H., & Bergman, Y. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2540 · Cited by 2,267 · see citing works

Dynamics and function of DNA methylation in plants

Zhang, H., Lang, Z., & Zhu, J. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0016-z · Cited by 1,829 · see citing works

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

Zemach, A., McDaniel, I. E., Silva, P., & Zilberman, D. (2010) · Science · doi:10.1126/science.1186366 · Cited by 1,796 · see citing works

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

Matzke, M. A., & Mosher, R. A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3683 · Cited by 1,662 · see citing works

BSMAP: whole genome bisulfite sequence MAPping program

Xi, Y., & Li, W. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-232 · Cited by 1,216 · see citing works

Dynamic changes in the human methylome during differentiationPreprint

Laurent, L. C., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C. T., Low, H. M., Sung, K. W. K., Rigoutsos, I., Loring, J. F., et al. (2010) · Genome Research · doi:10.1101/gr.101907.109 · Cited by 1,037 · see citing works

DNA methylation pathways and their crosstalk with histone methylation

Du, J., Johnson, L. M., Jacobsen, S. E., & Patel, D. J. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4043 · Cited by 1,000 · see citing works

Hhal methyltransferase flips its target base out of the DNA helix

Klimašauskas, S., Kumar, S., Roberts, R. J., & Cheng, X. (1994) · Cell · doi:10.1016/0092-8674(94)90342-5 · Cited by 945 · see citing works

Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation

Lindroth, A. M., Cao, X.-F., Jackson, J. P., Zilberman, D., McCallum, C., Henikoff, S., & Jacobsen, S. (2001) · Science · doi:10.1126/science.1059745 · Cited by 932 · see citing works

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

Stroud, H., Greenberg, M. V. C., Feng, S.-H., Bernatavichute, Y. V., & Jacobsen, S. (2013) · Cell · doi:10.1016/j.cell.2012.10.054 · Cited by 819 · see citing works

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Stroud, H., Do, T., Du, J.-M., Zhong, X., Feng, S.-H., Johnson, L., Patel, D., & Jacobsen, S. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2735 · Cited by 589 · see citing works

Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome

Xie, W., Barr, C. L., Kim, A., Yue, F., Lee, A. Y., Eubanks, J., Dempster, E. L., & Ren, B. (2012) · Cell · doi:10.1016/j.cell.2011.12.035 · Cited by 543 · see citing works

Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Directs DNA Methylation in Plants

Du, J.-M., Zhong, X., Bernatavichute, Y. V., Stroud, H., Feng, S.-H., Caro, E., Vashisht, A., Terragni, J., Chin, H., Tu, A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.034 · Cited by 496 · see citing works

The Site-Specific Installation of Methyl-Lysine Analogs into Recombinant Histones

Simon, M. D., Feixia Chu, C., Racki, L. R., de la Cruz, C. C., Burlingame, A. L., Panning, B., Narlikar, G. J., & Shokat, K. M. (2007) · Cell · doi:10.1016/j.cell.2006.12.041 · Cited by 475 · see citing works

A rapid and non‐destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana

Shimada, T. L., Shimada, T., & Hara‐Nishimura, I. (2009) · The Plant Journal · doi:10.1111/j.1365-313x.2009.04060.x · Cited by 423 · see citing works

The crystal structure of Haelll methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing

Reinisch, K. M., Chen, L., Verdine, G. L., & Lipscomb, W. N. (1995) · Cell · doi:10.1016/0092-8674(95)90060-8 · Cited by 366 · see citing works

Structural basis for DNMT3A-mediated de novo DNA methylation

Zhang, Z., Lu, R., Wang, P., Yu, Y., Chen, D., Gao, L., Liu, S., Ji, D., Rothbart, S. B., Wang, Y., et al. (2018) · Nature · doi:10.1038/nature25477 · Cited by 346 · see citing works

Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation

Song, J., Teplova, M., Ishibe-Murakami, S., & Patel, D. J. (2012) · Science · doi:10.1126/science.1214453 · Cited by 339 · see citing works

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNAPreprint

Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T. A., Reinders, J., Llaca, V., Deschamps, S., Smith, A. D., Levy, D., McCombie, W. R., et al. (2013) · Genome Research · doi:10.1101/gr.153510.112 · Cited by 265 · see citing works

Isolation and identification by sequence homology of a putative cytosine methyltransferase fromArabidopsis thaliana

Finnegan, E. J., & Dennis, E. S. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.10.2383 · Cited by 264 · see citing works

Non-CG Methylation in the Human Genome

He, Y., & Ecker, J. R. (2015) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090413-025437 · Cited by 263 · see citing works

A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis

Qian, W., Miki, D., Zhang, H., Liu, Y., Zhang, X., Tang, K., Kan, Y., La, H., Li, X., Li, S., et al. (2012) · Science · doi:10.1126/science.1219416 · Cited by 253 · see citing works

Modelling Extreme Stretching of DNA

Lebrun, A., & Lavery, R. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.12.2260 · Cited by 231 · see citing works

Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia

Xu, B., On, D. M., Ma, A., Parton, T., Konze, K. D., Pattenden, S. G., Allison, D. F., Cai, L., Rockowitz, S., Liu, S., et al. (2014) · Blood · doi:10.1182/blood-2014-06-581082 · Cited by 226 · see citing works

An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking

Ornstein, R. L., Rein, R., Breen, D. L., & MacElroy, R. D. (1978) · Biopolymers · doi:10.1002/bip.1978.360171005 · Cited by 217 · see citing works

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

Gao, L., Emperle, M., Guo, Y., Grimm, S. A., Ren, W., Adam, S., Uryu, H., Zhang, Z., Chen, D., Yin, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17109-4 · Cited by 198 · see citing works

The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications

Tang, K., Lang, Z., Zhang, H., & Zhu, J. (2016) · Nature Plants · doi:10.1038/nplants.2016.169 · Cited by 198 · see citing works

DNA Methylation Signatures of the Plant Chromomethyltransferases

Gouil, Q. A., & Baulcombe, D. C. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006526 · Cited by 177 · see citing works

Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation

Ren, W., Gao, L., & Song, J. (2018) · Genes · doi:10.3390/genes9120620 · Cited by 156 · see citing works

Maize Chromomethylase Zea methyltransferase2 Is Required for CpNpG Methylation

Papa, C. M., Springer, N. M., Muszynski, M. G., Meeley, R. B., & Kaeppler, S. M. (2001) · The Plant Cell · doi:10.1105/tpc.010064 · Cited by 139 · see citing works

Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis

Chen, C., Li, C., Wang, Y., Renaud, J. B., Tian, G., Kambhampati, S., Saatian, B., Nguyen, V., Hannoufa, A., Marsolais, F., et al. (2017) · Nature Plants · doi:10.1038/s41477-017-0023-7 · Cited by 115 · see citing works

5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase

Osterman, D. G., DePillis, G. D., Wu, J. C.-C., Matsuda, A., & Santi, D. V. (1988) · Biochemistry · doi:10.1021/bi00414a039 · Cited by 109 · see citing works

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

Zhang, C., Du, X., Tang, K., Yang, Z., Pan, L., Zhu, P., Luo, J., Jiang, Y., Zhang, H., Wan, H., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06965-w · Cited by 97 · see citing works

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

Adam, S., Anteneh, H., Hornisch, M., Wagner, V., Lu, J., Radde, N. E., Bashtrykov, P., Song, J., & Jeltsch, A. (2020) · Nature Communications · doi:10.1038/s41467-020-17531-8 · Cited by 89 · see citing works

Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation

Anteneh, H., Fang, J., & Song, J. (2020) · Nature Communications · doi:10.1038/s41467-020-16213-9 · Cited by 80 · see citing works

Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B

Lin, C.-C., Chen, Y., Yang, W., Shen, J., & Yuan, H. S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa111 · Cited by 58 · see citing works

A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase

Stoddard, C. I., Feng, S., Campbell, M. G., Liu, W., Wang, H., Zhong, X., Bernatavichute, Y. V., Cheng, Y., Jacobsen, S. E., & Narlikar, G. J. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.006 · Cited by 47 · see citing works

Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

Zabet, N. R., Catoni, M., Prischi, F., & Paszkowski, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1330 · Cited by 32 · see citing works

Substrate deformation regulates DRM2-mediated DNA methylation in plants

Fang, J., Leichter, S. M., Jiang, J., Biswal, M. N., Lu, J., Zhang, Z., Ren, W., Zhai, J., Cui, Q., Zhong, X., et al. (2021) · Science Advances · doi:10.1126/sciadv.abd9224 · Cited by 30 · see citing works

AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation inArabidopsis thaliana

Wang, Q., Bao, X., Chen, S., Zhong, H., Liu, Y., Zhang, L., Xia, Y., Kragler, F., Luo, M., Li, X., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab706 · Cited by 21 · see citing works

Generation of a luciferase-based reporter for CHH and CG DNA methylation inArabidopsis thaliana

Dinh, T. T., O'Leary, M. L., Won, S. Y., Li, S., Arroyo, L., Liu, X., Defries, A., Zheng, B., Cutler, S. R., & Chen, X. (2013) · Silence · doi:10.1186/1758-907x-4-1 · Cited by 19 · see citing works

Base Pair Opening in Three DNA-unwinding Elements

Coman, D., & Russu, I. M. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m502773200 · Cited by 18 · see citing works

Functions and Mechanisms of Histone Modifications in Plants

Le, H., Simmons, C. H., & Zhong, X. (2025) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-083123-070919 · Cited by 64 · see citing works

Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives

Majumder, S., Igamberdiev, A. U., & Debnath, S. C. (2025) · Agronomy · doi:10.3390/agronomy15061489 · Cited by 46 · see citing works

How transposable elements are recognized and epigenetically silenced in plants?

Liu, B., & Zhao, M. (2023) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2023.102428 · Cited by 39 · see citing works

Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants

Xie, G., Du, X., Hu, H., & Du, J. (2025) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-083123-054357 · Cited by 36 · see citing works

Harnessing transposable elements for plant functional genomics and genome engineering.

Tao, X.-Y., Feng, S.-L., Yuan, L., Li, Y.-J., Li, X.-J., Guan, X.-Y., Chen, Z.-H., & Xu, S. (2025) · Trends in Plant Science · doi:10.1016/j.tplants.2025.03.007 · Cited by 28 · see citing works

Epigenetic stress memory in gymnosperms

Fossdal, C. G., Krokene, P., Olsen, J. E., Strimbeck, R., Viejo, M. D., Yakovlev, I., & Magerøy, M. H. (2024) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiae051 · Cited by 29 · see citing works

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases

Jiang, J., Gwee, J., Fang, J., Leichter, S. M., Sanders, D., Ji, X., Song, J., & Zhong, X. (2024) · Science Advances · doi:10.1126/sciadv.adr2222 · Cited by 29 · see citing works

DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03222-w · Cited by 24 · see citing works

Recent Progress of Molecular Mechanisms of DNA Methylation in Plant Response to Abiotic Stress

Lu, X., Liu, Y., Xu, J., Liu, X., Chi, Y., Li, R., Mo, L., Shi, L., Liang, S., Yu, W., et al. (2024) · Environmental and Experimental Botany · doi:10.1016/j.envexpbot.2023.105599 · Cited by 22 · see citing works

Epiallelic variation of non-coding RNA genes and their phenotypic consequences

Liu, J., & Zhong, X.-H. (2024) · Nature Communications · doi:10.1038/s41467-024-45771-5 · Cited by 19 · see citing works

Population epigenetics: DNA methylation in the plant omics era

Liu, J., & Zhong, X. (2024) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiae089 · Cited by 19 · see citing works

Natural polymorphisms in ZMET2 encoding a DNA methyltransferase modulate the number of husk layers in maize

Wang, Z., Xia, A., Wang, Q., Cui, Z., Ming, L., Yu-sheng, Y., Wang, Y., & He, Y. (2024) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiae113 · Cited by 17 · see citing works

DNA conformational dynamics in the context-dependent non-CG CHH methylation by plant methyltransferase DRM2

Chen, J., Lu, J., Liu, J., Fang, J., Zhong, X., & Song, J. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105433 · Cited by 15 · see citing works

Unlocking bamboo's fast growth: Exploring the vital role of non‐structural carbohydrates (NSCs)

Chen, Y., Tang, M., Song, Y., Zargar, M., Chen, M., Lin, S., Zhu, F., & Song, T. (2025) · The Plant Journal · doi:10.1111/tpj.70147 · Cited by 14 · see citing works

DNA methylation dynamics: patterns, regulation, and function

Gwee, J., Tian, W., Qian, S., & Zhong, X. (2025) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2025.102787 · Cited by 14 · see citing works

Dynamic DNA methylation modifications in the cold stress response of cassava

Yu, G., Zhang, B., Chen, Q., Huang, Z., Zhang, B., Wang, K., & Han, J. (2024) · Genomics · doi:10.1016/j.ygeno.2024.110871 · Cited by 12 · see citing works

Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhizaPreprint

Dombey, R., Buendía-Ávila, D., Barragán‐Borrero, V., Diezma‐Navas, L., Ponce-Mañe, A., Vargas-Guerrero, J. M., Elias, R., & Marí‐Ordóñez, A. (2025) · Genome Research · doi:10.1101/gr.279532.124 · Cited by 14 · see citing works

Small RNA and Epigenetic Control of Plant Immunity

Wagh, S. G., Patil, A. M., Patil, G. B., Mankar, S. P., Rastogi, K., & Nishiguchi, M. (2025) · DNA · doi:10.3390/dna5040047 · Cited by 11 · see citing works

Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation

Shao, Z., Lu, J., Khudaverdyan, N., & Song, J. (2024) · Nature Communications · doi:10.1038/s41467-024-51246-4 · Cited by 12 · see citing works

An emerging role beyond genetics: DNA methylation in horticultural quality shaping

Chen, Y., Li, D., Lang, Z., Xu, Y., & Luo, Z. (2024) · The Innovation Life · doi:10.59717/j.xinn-life.2024.100050 · Cited by 9 · see citing works

Cryo-EM reveals evolutionarily conserved and distinct structural features of plant CG maintenance methyltransferase MET1

Kikuchi, A., Nishiyama, A., Chiba, Y., Nakanishi, M., To, T. K., & Arita, K. (2025) · Nature Communications · doi:10.1038/s41467-025-63765-9 · Cited by 9 · see citing works

An insight into tissue culture-induced variation origin shared between anther culture-derived triticale regenerants

Orłowska, R., Zimny, J., Żebrowski, J., Androsiuk, P., & Bednarek, P. T. (2024) · BMC Plant Biology · doi:10.1186/s12870-023-04679-w · Cited by 6 · see citing works

Structure of an Unfavorable de Novo DNA Methylation Complex of Plant Methyltransferase ZMET2

Herle, G., Fang, J., & Song, J. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169186 · Cited by 6 · see citing works

Structural insights into plant DNA CG methylation maintenance by MET1

Zhang, Z., Li, W., Liu, Y., Chi, C., Nan, J., Wang, C., Zhu, Y., Zhao, J., Xue, Y., Li, Y., et al. (2025) · The Plant Cell · doi:10.1093/plcell/koaf244 · Cited by 5 · see citing works

DNA methylation in monozygotic twins discordant for acute lymphoblastic leukemia: a case report and systematic review

Sun, M.-L., Li, Y., Man, R.-X., Wang, S., Guo, R., Yang, Y., & Pan, Y. (2025) · Clinical Epigenetics · doi:10.1186/s13148-025-01906-z · Cited by 4 · see citing works

Naturally Occurring Epialleles and Their Roles in Response to Climate Change in Birch

Chen, B., Zhang, T., Guo, Y., Cao, L., Zhang, X., Ali, S., Ma, R., Xie, L., Wang, J., Zinta, G., et al. (2025) · Molecular Ecology · doi:10.1111/mec.70031 · Cited by 4 · see citing works

Structure and autoinhibitory regulation of MET1 in the maintenance of plant CG methylation

Lu, J., Chen, X., Fang, J., Li, D., Le, H., Zhong, X., & Song, J. (2025) · The Plant Cell · doi:10.1093/plcell/koaf246 · Cited by 4 · see citing works

Homeostasis of DNA Hemi‐Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms

Chen, H., & Xu, C. (2025) · Advanced Science · doi:10.1002/advs.202505808 · Cited by 3 · see citing works

SHH1 cooperates with the DNA methylation reader MBD7 to suppress transcriptional silencing of promoter-methylated genes in Arabidopsis

Lu, Y., Jia, S., Guo, R., Wu, M.-S., Wang, H., Gao, S., Li, Z., Ma, Q., Hu, Y., Liu, C., et al. (2025) · Plant Communications · doi:10.1016/j.xplc.2025.101545 · Cited by 3 · see citing works

Epigenomic alterations and neural development anomalies in induced pluripotent stem cells from sporadic Alzheimer's disease

Katbe, A., Hanna, R., Flamier, A., Serhani, D., Hamam, R., Barabino, A., Tavares, E. S., Héon, E., & Bernier, G. (2025) · Development · doi:10.1242/dev.204910 · Cited by 3 · see citing works

5mC and 6mA DNA methylation in eukaryotic genomes

Nan, B., & Gao, S. (2026) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2026.01.002 · Cited by 3 · see citing works

Investigating the intercalation efficacy of sinomenine with diverse DNA fragments to understand its regulatory role in DNA methylation levels

Yao, Y.-D., Li, J.-M., Zhu, Z., Li, Q.-L., Luo, J.-F., Zhang, M.-X., Feng, C.-L., Deng, H., Pi, F.-C., Huang, S., et al. (2025) · Pharmacological Research · doi:10.1016/j.phrs.2025.108009 · Cited by 2 · see citing works

Linking cellular metabolism to chromatin modifications in plants

Hwang, J., & Seo, P. J. (2026) · Journal of Integrative Plant Biology · doi:10.1111/jipb.70150 · Cited by 2 · see citing works

Relationship between DNA methylation and ethylene in plants: A review

Geng, X., Liu, Z., An, C., Cao, M., Wang, Q., Liu, M., Li, Q., Wang, C., & Hu, L. (2026) · Plant Science · doi:10.1016/j.plantsci.2026.113063 · Cited by 2 · see citing works

Prediction of DNA Methylation With Long-Range State-Space Models

Feng, H., Chakravarty, S., & Lonardi, S. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2025.3634738 · Cited by 2 · see citing works

Dynamics of DNA methylation and histone acetylation and methylation during European chestnut bud development

Alves, S., Alhinho, A. T., Sobral, R. S., Costa, M. M. R., & Morais–Cecílio, L. (2025) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2025.110997 · Cited by 1 · see citing works

Chromosome‐scale genome assembly of the endangered aquatic plant Ottelia songmingensis elucidates genomic features and conservation implications

Li, Z., Qian, Z., Li, W., & Chen, J. (2026) · Journal of Systematics and Evolution · doi:10.1111/jse.70043 · Cited by 1 · see citing works

Genome-wide DNA methylation profiling of the octoploid strawberry (Fragaria × ananassa)

Jang, H., Han, H., Oh, Y., Han, K., Kim, D.-S., & Lee, S. (2026) · Epigenetics Insights · doi:10.48130/epi-0026-0002 · Cited by 1 · see citing works

Structural basis of water-mediated cis Watson–Crick/Hoogsteen base-pair formation in non-CpG methylation

Lin, S., Huang, H.-T., Fang, P.-J., Chang, C., Satange, R., Chang, C., Chou, S., Neidle, S., & Hou, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae594 · Cited by 1 · see citing works

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Lozano-Enguita, A., Baca-González, V., Morillas-Montaez, A., Pascual, J., Valledor, L., del Pozo, J. C., & Caro, E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.19.689328 · Cited by 1 · see citing works

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Liu, Q., Wang, Z., Cheng, X., Chen, Q., Zhang, Z., & Hang, H. E. (2026) · Research Square · doi:10.21203/rs.3.rs-9477401/v1 · Cited by 1 · see citing works

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Qi, X., Wang, Y., Zhang, X., Wei, X., Liu, X., Wang, Z., Wang, Z., & Ling, F. (2024) · Phyton · doi:10.32604/phyton.2024.052844

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Kaya, C. (2025) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2025.110640

Additional file 8 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26700721

Additional file 2 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25530385

Additional file 3 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26700706

Additional file 9 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26700724

Additional file 4 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26700709

Additional file 7 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26700718

Additional file 1 of An insight into tissue culture-induced variation origin shared between anther culture-derived triticale regenerants

Orłowska, R., Zimny, J., Żebrowski, J., Androsiuk, P., & Bednarek, P. T. (2024) · Figshare · doi:10.6084/m9.figshare.24979536

Additional file 1 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25530265

Additional file 5 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26700712

Additional file 6 of DNA methylation remodeling and the functional implication during male gametogenesis in rice

Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26700715

5-AzaC promotes the synthesis of patchoulol and pogostone in Pogostemon cablin by regulating DNA methylation

Yang, E., Lin, W., Chen, J., Yu, J., Xia, P., & Wang, Y. (2025) · Scientia Horticulturae · doi:10.1016/j.scienta.2025.114410

Epigenetic odyssey to decrypt the hidden code for sustainable brassica production: enhancing yield, stress resilience and nutritional quality

Maithreyi, R. S., Preet, S., Tanwar, K., Chakraborty, P., Gupta, I., Verma, R., Bharti, J., Thangaraj, A., Kaul, R., & Kaul, T. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2025.1696718

Phenotypic race profiling and cytosine methylation – Related gene expression in chickpea – Fusarium oxysporum f. sp. ciceris pathosystem

Talapov, T., AL-Saadi, A. R., Dedecan, O., Tanyolaç, B., & Can, C. (2026) · Physiological and Molecular Plant Pathology · doi:10.1016/j.pmpp.2026.103182

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Shi, Z., Han, Y., Liu, W., Wang, X., Tan, W., Zhao, W., Li, Z., Wang, Z., & Ai, P. (2026) · Industrial Crops and Products · doi:10.1016/j.indcrop.2026.123093

The SAUERKRAUT transposable element accelerates Arabidopsis floral transitionPreprint

Dongus, J. A., Tang, Y. H., van Driel, A. D., Schon, M. A., Pleunis, E. T., Duijts, K., Debnath, J., Koevoets, I. T., Kokkinopoulou, P., de Zeeuw, T., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.03.715599

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Guo, Y., Zhang, S., Li, Y., Zhang, X., Liu, J., Liu, J., Fan, L., Qin, M., & Wang, G. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2026.1781873

A role of protein conformational dynamics in mammalian DNA methylation

Song, J. (2026) · Structural Dynamics · doi:10.1063/4.0001204

Epigenetics in Crop Abiotic Stress Adaptation and Memory

Kumar, P., & Gahlaut, V. (2026) · Springer eBooks · doi:10.1007/978-981-95-7680-7_7

Evolutionary dynamics and functional divergence of DNA methyltransferase in Poaceae

Hai, J.-H., Lei, J.-Q., Han, Q., Feng, Y., Yu, H., & Li, L. (2026) · Journal of Systematics and Evolution · doi:10.1111/jse.70082

Effectiveness of epigenetics in addressing climate change effects and the growing food demand

Obedgiu, S., Gaoua, O., Zahid, S. M., & Salad, F. Y. (2026) · Discover Agriculture · doi:10.1007/s44279-026-00588-2

Integrated methylome and transcriptome analysis provides insight into DNA methylation-mediated networks in sexual dimorphism of Vernicia montana

Dong, X., Zhang, L., 朱华国, Peng, J., Lu, C., & Li, W. (2026) · BMC Plant Biology · doi:10.1186/s12870-026-09376-y

Disruption of lysine biosynthesis modulates DNA methylation and developmental programs in Arabidopsis thalianaPreprint

Araújo, W. L., Gouveia, D. G., Flachbart, S., Barrios, W. E. B., Westhoff, P., Reis, P. A. B., Fernie, A. R., Nunes‐Nesi, A., & Weber, A. P. M. (2026) · Research Square · doi:10.21203/rs.3.rs-10021158/v1

Codon Usage Bias Shapes CpG Architecture in Millet Coding SequencesPreprint

Bevin Nishanth, J., & Somasundaram, S. (2026) · Research Square · doi:10.21203/rs.3.rs-9956333/v1

Crosstalk between plant proteostasis and chromatin remodelling machinery

Albacete-Rodríguez, M., & Rubio, V. (2026) · Journal of Experimental Botany · doi:10.1093/jxb/erag273

Integrative methylome and transcriptome analysis reveals genotype and sequence context-specific responses to aluminum stress in rice

Gallo‐Franco, J. J., Sosa, C. C., Johannes, F. M., Ghneim‐Herrera, T., & Quimbaya, M. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2026.1896320

Transposable elements and their epigenetic modifications mediate gene expression and subgenome dominance in Brassica carinata

Li, G., Zhu, S., Li, J., Kong, F., & Wang, J. (2026) · Theoretical and Applied Genetics · doi:10.1007/s00122-026-05349-9

Chromatin homogenization triggers burst of CHH methylation in soybean

Cao, L., Zhang, T., Ma, S., Wang, L., Wang, W., Zhang, P., Wang, M., Chen, B., Zhang, Z., Guo, Y., et al. (2026) · The Plant Cell · doi:10.1093/plcell/koag250

Long-term lithium exposure induces persistent physiological and methylation-associated alterations in Chromochloris zofingiensis: An integrated multi-omics analysis

Feng, R., Zhang, Z., 水小溪, Wang, J., Wang, C., Pengda, Y., Zhang, Z., Zhao, B., & Sun, D. (2026) · Environmental Pollution · doi:10.1016/j.envpol.2026.129018

DNA Methylation-Mediated Regulation of Plant Adaptation to Abiotic Stress

Liu, G., Wang, H., Tang, Y., Gao, H., Wang, Y., Sun, Y., Yu, S., Zhang, D., & Jiang, Z. (2026) · Plants · doi:10.3390/plants15203166

Combined Abiotic Stress Rewires DNA Methylation to Modulate Regulatory Potential Rather Than Transcription in Arabidopsis

Lozano-Enguita, A., Morillas-Montaez, A., Baca-González, V., Pascual, J., Valledor, L., del Pozo, J. C., & Caro, E. (2026) · Plant Cell & Environment · doi:10.1111/pce.70985

Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Directs DNA Methylation in Plants

Du, J.-M., Zhong, X., Bernatavichute, Y. V., Stroud, H., Feng, S.-H., Caro, E., Vashisht, A., Terragni, J., Chin, H., Tu, A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.034 · Cited by 496 · see citing works

Structure of an Unfavorable de Novo DNA Methylation Complex of Plant Methyltransferase ZMET2

Herle, G., Fang, J., & Song, J. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169186 · Cited by 6 · see citing works

Maintenance and Inheritance of DNA Methylation in Arabidopsis

Hsieh, P.-H. (2016) · eScholarship (California Digital Library) · Cited by 2 · see citing works

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases

Jiang, J., Gwee, J., Fang, J., Leichter, S. M., Sanders, D., Ji, X., Song, J., & Zhong, X. (2024) · Science Advances · doi:10.1126/sciadv.adr2222 · Cited by 29 · see citing works

Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3

Lindroth, A. M., Shultis, D., Jasencakova, Z., Fuchs, J., Johnson, L. M., Schubert, D. S. P., Patnaik, D., Pradhan, S., Goodrich, J., Schubert, I. A., et al. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600430 · Cited by 359 · see citing works