Mechanistic basis for maintenance of CHG DNA methylation in plants

Fang, Jian; Jiang, Jianjun; Leichter, Sarah M.; Liu, Jie; Biswal, Mahamaya; Khudaverdyan, Nelli; Zhong, Xuehua; Song, Jikui

doi:10.1038/s41467-022-31627-3

Mechanistic basis for maintenance of CHG DNA methylation in plants

Journal Article · 01 July 2022 · Nat. Commun.

DOI:https://doi.org/10.1038/s41467-022-31627-3· OSTI ID:1900637

Fang, Jian; Jiang, Jianjun; Leichter, Sarah M.; Liu, Jie; Biswal, Mahamaya; Khudaverdyan, Nelli; Zhong, Xuehua; Song, Jikui

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIH

OSTI ID:: 1900637

Journal Information:: Nat. Commun., Journal Name: Nat. Commun. Vol. 13

Country of Publication:: United States

Language:: ENGLISH

References (55)

Hhal methyltransferase flips its target base out of the DNA helix Klimasauskas, Saulius; Kumar, Sanjay; Roberts, Richard J. Cell, Vol. 76, Issue 2 https://doi.org/10.1016/0092-8674(94)90342-5	journal	January 1994
Establishing, maintaining and modifying DNA methylation patterns in plants and animals Law, Julie A.; Jacobsen, Steven E. Nature Reviews Genetics, Vol. 11, Issue 3 https://doi.org/10.1038/nrg2719	journal	February 2010
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning Cokus, Shawn J.; Feng, Suhua; Zhang, Xiaoyu Nature, Vol. 452, Issue 7184 https://doi.org/10.1038/nature06745	journal	February 2008
Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation Anteneh, Hiwot; Fang, Jian; Song, Jikui Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16213-9	journal	May 2020
Linking DNA methylation and histone modification: patterns and paradigms Cedar, Howard; Bergman, Yehudit Nature Reviews Genetics, Vol. 10, Issue 5 https://doi.org/10.1038/nrg2540	journal	May 2009
The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications Tang, Kai; Lang, Zhaobo; Zhang, Heng Nature Plants, Vol. 2, Issue 11 https://doi.org/10.1038/nplants.2016.169	journal	October 2016
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
The Site-Specific Installation of Methyl-Lysine Analogs into Recombinant Histones Simon, Matthew D.; Chu, Feixia; Racki, Lisa R. Cell, Vol. 128, Issue 5 https://doi.org/10.1016/j.cell.2006.12.041	journal	March 2007
An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking Ornstein, Rick L.; Rein, Robert; Breen, Donnal L. Biopolymers, Vol. 17, Issue 10 https://doi.org/10.1002/bip.1978.360171005	journal	October 1978
Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation Lindroth, A. M. Science, Vol. 292, Issue 5524 https://doi.org/10.1126/science.1059745	journal	May 2001
A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis Qian, W.; Miki, D.; Zhang, H. Science, Vol. 336, Issue 6087 https://doi.org/10.1126/science.1219416	journal	June 2012
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants Du, Jiamu; Zhong, Xuehua; Bernatavichute, Yana V. Cell, Vol. 151, Issue 1 https://doi.org/10.1016/j.cell.2012.07.034	journal	September 2012
Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome Xie, Wei; Barr, Cathy L.; Kim, Audrey Cell, Vol. 148, Issue 4 https://doi.org/10.1016/j.cell.2011.12.035	journal	February 2012
Non-CG Methylation in the Human Genome He, Yupeng; Ecker, Joseph R. Annual Review of Genomics and Human Genetics, Vol. 16, Issue 1 https://doi.org/10.1146/annurev-genom-090413-025437	journal	August 2015
Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation Zemach, A.; McDaniel, I. E.; Silva, P. Science, Vol. 328, Issue 5980 https://doi.org/10.1126/science.1186366	journal	April 2010
deepTools: a flexible platform for exploring deep-sequencing data Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku365	journal	May 2014
The crystal structure of Haelll methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing Reinisch, Karin M.; Chen, Lin; Verdine, Gregory L. Cell, Vol. 82, Issue 1 https://doi.org/10.1016/0092-8674(95)90060-8	journal	July 1995
The language of covalent histone modifications Strahl, Brian D.; Allis, C. David Nature, Vol. 403, Issue 6765 https://doi.org/10.1038/47412	journal	January 2000
Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation Song, J.; Teplova, M.; Ishibe-Murakami, S. Science, Vol. 335, Issue 6069 https://doi.org/10.1126/science.1214453	journal	February 2012
Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia Xu, Bowen; On, Doan M.; Ma, Anqi Blood, Vol. 125, Issue 2 https://doi.org/10.1182/blood-2014-06-581082	journal	January 2015
DNA methylation patterns and epigenetic memory Bird, A. Genes & Development, Vol. 16, Issue 1 https://doi.org/10.1101/gad.947102	journal	January 2002
Substrate deformation regulates DRM2-mediated DNA methylation in plants Fang, Jian; Leichter, Sarah M.; Jiang, Jianjun Science Advances, Vol. 7, Issue 23 https://doi.org/10.1126/sciadv.abd9224	journal	June 2021
5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase Osterman, David G.; DePillis, Gia D.; Wu, John C. Biochemistry, Vol. 27, Issue 14 https://doi.org/10.1021/bi00414a039	journal	July 1988
RNA-directed DNA methylation: an epigenetic pathway of increasing complexity Matzke, Marjori A.; Mosher, Rebecca A. Nature Reviews Genetics, Vol. 15, Issue 6 https://doi.org/10.1038/nrg3683	journal	May 2014
PHENIX : building new software for automated crystallographic structure determination Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11 https://doi.org/10.1107/S0907444902016657	journal	October 2002
Generation of a luciferase-based reporter for CHH and CG DNA methylation inArabidopsis thaliana Dinh, Thanh Theresa; O’Leary, Michael; Won, So Youn Silence, Vol. 4, Issue 1 https://doi.org/10.1186/1758-907X-4-1	journal	April 2013
A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase Stoddard, Caitlin I.; Feng, Suhua; Campbell, Melody G. Molecular Cell, Vol. 73, Issue 1 https://doi.org/10.1016/j.molcel.2018.10.006	journal	January 2019
Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis Chen, Chen; Li, Chenlong; Wang, Ying Nature Plants, Vol. 3, Issue 10 https://doi.org/10.1038/s41477-017-0023-7	journal	September 2017
Maize Chromomethylase Zea methyltransferase2 Is Required for CpNpG Methylation Papa, Charles M.; Springer, Nathan M.; Muszynski, Michael G. The Plant Cell, Vol. 13, Issue 8 https://doi.org/10.1105/TPC.010064	journal	August 2001
Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana Jean Finnegan, E.; Dennis, Elizabeth S. Nucleic Acids Research, Vol. 21, Issue 10 https://doi.org/10.1093/nar/21.10.2383	journal	January 1993
Dynamic changes in the human methylome during differentiation Laurent, L.; Wong, E.; Li, G. Genome Research, Vol. 20, Issue 3 https://doi.org/10.1101/gr.101907.109	journal	February 2010
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Fast and accurate short read alignment with Burrows-Wheeler transform Li, H.; Durbin, R. Bioinformatics, Vol. 25, Issue 14 https://doi.org/10.1093/bioinformatics/btp324	journal	May 2009
AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana Wang, Qianwen; Bao, Xiucong; Chen, Shengjie Nucleic Acids Research, Vol. 49, Issue 17 https://doi.org/10.1093/nar/gkab706	journal	August 2021
Model-based Analysis of ChIP-Seq (MACS) Zhang, Yong; Liu, Tao; Meyer, Clifford A. Genome Biology, Vol. 9, Issue 9 https://doi.org/10.1186/gb-2008-9-9-r137	journal	January 2008
Dynamics and function of DNA methylation in plants Zhang, Huiming; Lang, Zhaobo; Zhu, Jian-Kang Nature Reviews Molecular Cell Biology, Vol. 19, Issue 8 https://doi.org/10.1038/s41580-018-0016-z	journal	May 2018
Modelling Extreme Stretching of DNA Lebrun, A.; Lavery, R. Nucleic Acids Research, Vol. 24, Issue 12 https://doi.org/10.1093/nar/24.12.2260	journal	June 1996
Human DNA methylomes at base resolution show widespread epigenomic differences Lister, Ryan; Pelizzola, Mattia; Dowen, Robert H. Nature, Vol. 462, Issue 7271 https://doi.org/10.1038/nature08514	journal	October 2009
Base Pair Opening in Three DNA-unwinding Elements Coman, Daniel; Russu, Irina M. Journal of Biological Chemistry, Vol. 280, Issue 21 https://doi.org/10.1074/jbc.M502773200	journal	May 2005
Structural basis for DNMT3A-mediated de novo DNA methylation Zhang, Zhi-Min; Lu, Rui; Wang, Pengcheng Nature, Vol. 554, Issue 7692 https://doi.org/10.1038/nature25477	journal	February 2018
BSMAP: whole genome bisulfite sequence MAPping program Xi, Yuanxin; Li, Wei BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-232	journal	July 2009
DNA Methylation Signatures of the Plant Chromomethyltransferases Gouil, Quentin; Baulcombe, David C. PLOS Genetics, Vol. 12, Issue 12 https://doi.org/10.1371/journal.pgen.1006526	journal	December 2016
DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation Adam, Sabrina; Anteneh, Hiwot; Hornisch, Maximilian Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-17531-8	journal	July 2020
fastp: an ultra-fast all-in-one FASTQ preprocessor Chen, Shifu; Zhou, Yanqing; Chen, Yaru Bioinformatics, Vol. 34, Issue 17 https://doi.org/10.1093/bioinformatics/bty560	journal	September 2018
Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis Stroud, Hume; Do, Truman; Du, Jiamu Nature Structural & Molecular Biology, Vol. 21, Issue 1 https://doi.org/10.1038/nsmb.2735	journal	December 2013
Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin Zhang, Cuijun; Du, Xuan; Tang, Kai Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06965-w	journal	October 2018
A rapid and non-destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana Shimada, Takashi L.; Shimada, Tomoo; Hara-Nishimura, Ikuko The Plant Journal, Vol. 61, Issue 3 https://doi.org/10.1111/j.1365-313X.2009.04060.x	journal	February 2010
Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms Gao, Linfeng; Emperle, Max; Guo, Yiran Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-17109-4	journal	July 2020
Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B Lin, Chien-Chu; Chen, Yi-Ping; Yang, Wei-Zen Nucleic Acids Research, Vol. 48, Issue 7 https://doi.org/10.1093/nar/gkaa111	journal	February 2020
Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation Ren, Wendan; Gao, Linfeng; Song, Jikui Genes, Vol. 9, Issue 12 https://doi.org/10.3390/genes9120620	journal	December 2018
DNA methylation pathways and their crosstalk with histone methylation Du, Jiamu; Johnson, Lianna M.; Jacobsen, Steven E. Nature Reviews Molecular Cell Biology, Vol. 16, Issue 9 https://doi.org/10.1038/nrm4043	journal	August 2015
Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome Stroud, Hume; Greenberg, Maxim V. C.; Feng, Suhua Cell, Vol. 152, Issue 1-2 https://doi.org/10.1016/j.cell.2012.10.054	journal	January 2013
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA Regulski, M.; Lu, Z.; Kendall, J. Genome Research, Vol. 23, Issue 10 https://doi.org/10.1101/gr.153510.112	journal	June 2013

Similar Records

Mechanistic basis for maintenance of CHG DNA methylation in plants

Journal Article · 2022 · Nat. Commun. · OSTI ID:1879700

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

Journal Article · 2012 · Science · OSTI ID:1035701

Structural basis for Klf4 recognition of methylated DNA

Journal Article · 2014 · Nucleic Acids Res. · OSTI ID:1131347

Mechanistic basis for maintenance of CHG DNA methylation in plants

Citation Formats

References (55)

Similar Records

Related Subjects