Mechanistic basis for maintenance of CHG DNA methylation in plants.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
05 07 2022
05 07 2022
Historique:
received:
15
10
2021
accepted:
26
06
2022
entrez:
5
7
2022
pubmed:
6
7
2022
medline:
8
7
2022
Statut:
epublish
Résumé
DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, DNA methylation widely occurs in the CG, CHG, and CHH (H = A, C, or T) contexts, with the maintenance of CHG methylation mediated by CMT3 chromomethylase. However, how CMT3 interacts with the chromatin environment for faithful maintenance of CHG methylation is unclear. Here we report structure-function characterization of the H3K9me2-directed maintenance of CHG methylation by CMT3 and its Zea mays ortholog ZMET2. Base-specific interactions and DNA deformation coordinately underpin the substrate specificity of CMT3 and ZMET2, while a bivalent readout of H3K9me2 and H3K18 allosterically stimulates substrate binding. Disruption of the interaction with DNA or H3K9me2/H3K18 led to loss of CMT3/ZMET2 activity in vitro and impairment of genome-wide CHG methylation in vivo. Together, our study uncovers how the intricate interplay of CMT3, repressive histone marks, and DNA sequence mediates heterochromatic CHG methylation.
Identifiants
pubmed: 35790763
doi: 10.1038/s41467-022-31627-3
pii: 10.1038/s41467-022-31627-3
pmc: PMC9256654
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
3877Subventions
Organisme : NIAID NIH HHS
ID : R21 AI147057
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM124806
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM119721
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007133
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008349
Pays : United States
Informations de copyright
© 2022. The Author(s).
Références
Nat Rev Mol Cell Biol. 2018 Aug;19(8):489-506
pubmed: 29784956
Nucleic Acids Res. 1993 May 25;21(10):2383-8
pubmed: 8389441
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Nat Struct Mol Biol. 2014 Jan;21(1):64-72
pubmed: 24336224
Nat Commun. 2020 May 8;11(1):2294
pubmed: 32385248
Nucleic Acids Res. 1996 Jun 15;24(12):2260-7
pubmed: 8710494
Genes (Basel). 2018 Dec 11;9(12):
pubmed: 30544982
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Nat Rev Genet. 2009 May;10(5):295-304
pubmed: 19308066
Nucleic Acids Res. 2020 Apr 17;48(7):3949-3961
pubmed: 32083663
BMC Bioinformatics. 2009 Jul 27;10:232
pubmed: 19635165
Cell. 1995 Jul 14;82(1):143-53
pubmed: 7606780
Cell. 2012 Feb 17;148(4):816-31
pubmed: 22341451
Nat Rev Mol Cell Biol. 2015 Sep;16(9):519-32
pubmed: 26296162
Nucleic Acids Res. 2021 Sep 27;49(17):9755-9767
pubmed: 34403482
Science. 2012 Jun 15;336(6087):1445-8
pubmed: 22700931
Nat Rev Genet. 2010 Mar;11(3):204-20
pubmed: 20142834
Genome Res. 2010 Mar;20(3):320-31
pubmed: 20133333
Nat Rev Genet. 2014 Jun;15(6):394-408
pubmed: 24805120
Biopolymers. 1978 Oct;17(10):2341-60
pubmed: 24624489
Blood. 2015 Jan 8;125(2):346-57
pubmed: 25395428
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Annu Rev Genomics Hum Genet. 2015;16:55-77
pubmed: 26077819
Silence. 2013 Apr 05;4(1):1
pubmed: 23561294
J Biol Chem. 2005 May 27;280(21):20216-21
pubmed: 15784615
Methods Enzymol. 1997;276:307-26
pubmed: 27754618
Cell. 2012 Sep 28;151(1):167-80
pubmed: 23021223
Cell. 2013 Jan 17;152(1-2):352-64
pubmed: 23313553
Plant Cell. 2001 Aug;13(8):1919-28
pubmed: 11487702
Nature. 2009 Nov 19;462(7271):315-22
pubmed: 19829295
Nat Commun. 2018 Oct 31;9(1):4547
pubmed: 30382101
Nature. 2008 Mar 13;452(7184):215-9
pubmed: 18278030
Nature. 2018 Feb 15;554(7692):387-391
pubmed: 29414941
Science. 2001 Jun 15;292(5524):2077-80
pubmed: 11349138
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Cell. 2007 Mar 9;128(5):1003-12
pubmed: 17350582
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
pubmed: 15572765
Science. 2010 May 14;328(5980):916-9
pubmed: 20395474
Nat Plants. 2017 Oct;3(10):814-824
pubmed: 28947800
Plant J. 2010 Feb 1;61(3):519-28
pubmed: 19891705
Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54
pubmed: 12393927
PLoS Genet. 2016 Dec 20;12(12):e1006526
pubmed: 27997534
Nature. 2000 Jan 6;403(6765):41-5
pubmed: 10638745
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91
pubmed: 24799436
Science. 2012 Feb 10;335(6069):709-12
pubmed: 22323818
Nat Commun. 2020 Jul 24;11(1):3723
pubmed: 32709850
Biochemistry. 1988 Jul 12;27(14):5204-10
pubmed: 3167042
Nucleic Acids Res. 2017 Apr 20;45(7):3777-3784
pubmed: 28053115
Mol Cell. 2019 Jan 3;73(1):73-83.e6
pubmed: 30415948
Nat Commun. 2020 Jul 3;11(1):3355
pubmed: 32620778
Cell. 1994 Jan 28;76(2):357-69
pubmed: 8293469
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
pubmed: 19461840
Nat Plants. 2016 Oct 31;2(11):16169
pubmed: 27797352
Sci Adv. 2021 Jun 2;7(23):
pubmed: 34078593
Genome Res. 2013 Oct;23(10):1651-62
pubmed: 23739895
Genes Dev. 2002 Jan 1;16(1):6-21
pubmed: 11782440