RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
08 04 2019
08 04 2019
Historique:
received:
03
11
2018
accepted:
13
03
2019
entrez:
10
4
2019
pubmed:
10
4
2019
medline:
14
6
2019
Statut:
epublish
Résumé
To properly regulate the genome, cytosine methylation is established by animal DNA methyltransferase 3 s (DNMT3s). While altered DNMT3 homologs, Domains rearranged methyltransferases (DRMs), have been shown to establish methylation via the RNA directed DNA methylation (RdDM) pathway, the role of true-plant DNMT3 orthologs remains elusive. Here, we profile de novo (RPS transgene) and genomic methylation in the basal plant, Physcomitrella patens, mutated in each of its PpDNMTs. We show that PpDNMT3b mediates CG and CHH de novo methylation, independently of PpDRMs. Complementary de novo CHG methylation is specifically mediated by the CHROMOMETHYLASE, PpCMT. Intragenomically, PpDNMT3b functions preferentially within heterochromatin and is affected by PpCMT. In comparison, PpDRMs target active-euchromatic transposons. Overall, our data resolve how DNA methylation in plants can be established in heterochromatin independently of RdDM; suggest that DRMs have emerged to target euchromatin; and link DNMT3 loss in angiosperms to the initiation of heterochromatic CHH methylation by CMT2.
Identifiants
pubmed: 30962443
doi: 10.1038/s41467-019-09496-0
pii: 10.1038/s41467-019-09496-0
pmc: PMC6453930
doi:
Substances chimiques
Heterochromatin
0
Plant Proteins
0
DNA (Cytosine-5-)-Methyltransferases
EC 2.1.1.37
chromomethylase
EC 2.1.1.37
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1613Commentaires et corrections
Type : ErratumIn
Références
Nat Rev Mol Cell Biol. 2015 Sep;16(9):519-32
pubmed: 26296162
PLoS Genet. 2011 Jul;7(7):e1002195
pubmed: 21811420
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14728-33
pubmed: 26553984
Plant J. 2014 Jul;79(1):67-81
pubmed: 24779858
Cell. 2014 Mar 13;156(6):1286-1297
pubmed: 24630728
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Annu Rev Biochem. 2005;74:481-514
pubmed: 15952895
EMBO J. 2006 Jun 21;25(12):2828-36
pubmed: 16724114
Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4979-84
pubmed: 10781108
Plant Mol Biol. 2004 Apr;54(6):793-804
pubmed: 15604652
Plant Mol Biol. 2015 Jul;88(4-5):387-400
pubmed: 25944663
Mol Plant. 2018 Mar 5;11(3):381-387
pubmed: 29032247
Trends Plant Sci. 2018 Jul;23(7):598-612
pubmed: 29703667
Genome Biol. 2009;10(3):R25
pubmed: 19261174
Adv Exp Med Biol. 2016;945:87-122
pubmed: 27826836
Nat Struct Mol Biol. 2012 Sep;19(9):870-5
pubmed: 22864289
Nat Rev Genet. 2014 Jun;15(6):394-408
pubmed: 24805120
Curr Opin Plant Biol. 2017 Apr;36:135-141
pubmed: 28343122
Proc Natl Acad Sci U S A. 2018 May 15;115(20):E4720-E4729
pubmed: 29712855
Science. 2012 Sep 14;337(6100):1360-1364
pubmed: 22984074
Plant Cell. 2015 Aug;27(8):2148-62
pubmed: 26209555
Annu Rev Genomics Hum Genet. 2015;16:55-77
pubmed: 26077819
Nat Plants. 2016 Nov 03;2(11):16163
pubmed: 27808230
Genome Biol Evol. 2015 Sep 02;7(9):2648-62
pubmed: 26338185
Gigascience. 2014 Oct 27;3:17
pubmed: 25625010
Annu Rev Genet. 2015;49:439-59
pubmed: 26631514
Genome Res. 2016 Aug;26(8):1057-68
pubmed: 27225844
Plant J. 2018 Feb;93(3):515-533
pubmed: 29237241
Cell. 2012 Sep 28;151(1):167-80
pubmed: 23021223
Plant Mol Biol. 2002 Mar;48(4):383-99
pubmed: 11905965
DNA Res. 2000 Feb 28;7(1):9-17
pubmed: 10718194
Cell. 2013 Mar 28;153(1):193-205
pubmed: 23540698
EMBO J. 2011 May 18;30(10):1928-38
pubmed: 21487388
Nat Struct Mol Biol. 2014 Jan;21(1):64-72
pubmed: 24336224
Plant Biol (Stuttg). 2005 May;7(3):220-7
pubmed: 15912441
Proc Natl Acad Sci U S A. 2010 May 11;107(19):8689-94
pubmed: 20395551
Genome Biol. 2017 May 1;18(1):65
pubmed: 28457232
Cell. 2013 Jan 17;152(1-2):352-64
pubmed: 23313553
Plant Cell. 2016 Feb;28(2):314-25
pubmed: 26869701
G3 (Bethesda). 2018 May 31;8(6):1921-1932
pubmed: 29618467
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
pubmed: 21062823
Plant J. 2012 Sep;71(6):1029-37
pubmed: 22587613
Nature. 2008 Mar 13;452(7184):215-9
pubmed: 18278030
Ecol Lett. 2017 Dec;20(12):1576-1590
pubmed: 29027325
Annu Rev Biochem. 2012;81:97-117
pubmed: 22404632
Plant J. 2008 Dec;56(5):814-23
pubmed: 18665914
Science. 2010 May 14;328(5980):916-9
pubmed: 20395474
New Phytol. 2018 Jan;217(2):540-546
pubmed: 29105762
Genome Biol. 2018 Jan 25;19(1):9
pubmed: 29368664
Mol Biol Evol. 2018 Feb 1;35(2):518-522
pubmed: 29077904
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
PLoS Genet. 2016 Dec 20;12(12):e1006526
pubmed: 27997534
Trends Plant Sci. 2017 May;22(5):351-353
pubmed: 28392157
Plant Mol Biol. 2014 Apr;84(6):719-35
pubmed: 24370935
Genome Biol. 2016 Sep 27;17(1):194
pubmed: 27671052
Annu Rev Plant Biol. 2015;66:243-67
pubmed: 25494460
PLoS One. 2013 May 06;8(5):e63652
pubmed: 23671690
Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):9111-6
pubmed: 27457936
Science. 2008 Jan 4;319(5859):64-9
pubmed: 18079367
BMC Genomics. 2013 Jul 23;14:498
pubmed: 23879659
Eur J Biochem. 2002 Oct;269(20):4981-4
pubmed: 12383256
FEBS J. 2012 Nov;279(21):4081-94
pubmed: 22943564
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68
pubmed: 25355905
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W5-9
pubmed: 18440982
Plant Physiol. 2016 Jul;171(3):2041-54
pubmed: 27208249
Nat Genet. 2017 Jul;49(7):1099-1106
pubmed: 28581499