Domains Rearranged Methylase 2 maintains DNA methylation at large DNA hypomethylated shores and long-range chromatin interactions in rice.
OsDRM2
3D genome architectures
ChIA-PET
DNA methylation
H3K27me3
NORG
Journal
Plant biotechnology journal
ISSN: 1467-7652
Titre abrégé: Plant Biotechnol J
Pays: England
ID NLM: 101201889
Informations de publication
Date de publication:
11 2023
11 2023
Historique:
revised:
25
06
2023
received:
09
03
2023
accepted:
08
07
2023
medline:
23
10
2023
pubmed:
4
8
2023
entrez:
4
8
2023
Statut:
ppublish
Résumé
DNA methylation plays an important role in gene regulation and genomic stability. However, large DNA hypomethylated regions known as DNA methylation valleys (DMVs) or canyons have also been suggested to serve unique regulatory functions, largely unknown in rice (Oryza sativa). Here, we describe the DMVs in rice seedlings, which were highly enriched with developmental and transcription regulatory genes. Further detailed analysis indicated that grand DMVs (gDMVs) might be derived from nuclear integrants of organelle DNA (NORGs). Furthermore, Domains Rearranged Methylase 2 (OsDRM2) maintained DNA methylation at short DMV (sDMV) shores. Epigenetic maps indicated that sDMVs were marked with H3K4me3 and/or H3K27me3, although the loss of DNA methylation had a negligible effect on histone modification within these regions. In addition, we constructed H3K27me3-associated interaction maps for homozygous T-DNA insertion mutant of the gene (osdrm2) and wild type (WT). From a global perspective, most (90%) compartments were stable between osdrm2 and WT plants. At a high resolution, we observed a dramatic loss of long-range chromatin loops in osdrm2, which suffered an extensive loss of non-CG (CHG and CHH, H = A, T, or C) methylation. From another viewpoint, the loss of non-CG methylation at sDMV shores in osdrm2 could disrupt H3K27me3-mediated chromatin interaction networks. Overall, our results demonstrated that DMVs are a key genomic feature in rice and are precisely regulated by epigenetic modifications, including DNA methylation and histone modifications. OsDRM2 maintained DNA methylation at sDMV shores, while OsDRM2 deficiency strongly affected three-dimensional (3D) genome architectures.
Identifiants
pubmed: 37539491
doi: 10.1111/pbi.14134
pmc: PMC10579712
doi:
Substances chimiques
Chromatin
0
Histones
0
Plant Proteins
0
Methyltransferases
EC 2.1.1.-
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2333-2347Informations de copyright
© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Références
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
Cell. 2013 Mar 28;153(1):193-205
pubmed: 23540698
Mol Biol Evol. 2021 Aug 23;38(9):3621-3636
pubmed: 33973633
Genome Biol. 2010;11(2):R22
pubmed: 20181287
Genome Biol. 2008;9(9):R137
pubmed: 18798982
FEBS J. 2009 Nov;276(21):6301-11
pubmed: 19788421
Cell. 2013 May 23;153(5):1134-48
pubmed: 23664764
Nature. 2009 Nov 5;462(7269):58-64
pubmed: 19890323
Plant Mol Biol. 2019 May;100(1-2):33-46
pubmed: 30788769
J Integr Plant Biol. 2022 Dec;64(12):2396-2410
pubmed: 36194511
Nat Genet. 2019 Jan;51(1):96-105
pubmed: 30478443
Nat Commun. 2019 May 2;10(1):2063
pubmed: 31048693
Mol Cell Biol. 2015 Nov 23;36(3):452-61
pubmed: 26598602
Epigenetics. 2011 Feb;6(2):147-52
pubmed: 20935486
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Genome Biol. 2013 Aug 29;14(8):R91
pubmed: 23987249
Innovation (Camb). 2021 Jul 01;2(3):100141
pubmed: 34557778
Nat Rev Genet. 2010 Mar;11(3):204-20
pubmed: 20142834
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Plant J. 2018 Jun;94(6):1141-1156
pubmed: 29660196
G3 (Bethesda). 2021 Apr 15;11(4):
pubmed: 33617633
Nat Rev Mol Cell Biol. 2018 Aug;19(8):489-506
pubmed: 29784956
Mol Plant. 2021 Oct 4;14(10):1757-1767
pubmed: 34171480
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
BMC Bioinformatics. 2019 Jan 22;20(1):47
pubmed: 30669962
Mol Cell. 2014 Sep 4;55(5):694-707
pubmed: 25132175
Plant Cell. 2021 Sep 24;33(9):2950-2964
pubmed: 34117872
Cell Rep. 2019 Nov 12;29(7):1974-1985.e6
pubmed: 31722211
Mol Cell. 2020 May 7;78(3):506-521.e6
pubmed: 32386543
Nat Methods. 2016 Nov;13(11):919-922
pubmed: 27643841
Genome Res. 2012 Jun;22(6):1128-38
pubmed: 22466170
Genome Res. 2012 Sep;22(9):1813-31
pubmed: 22955991
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nat Genet. 2009 Feb;41(2):178-186
pubmed: 19151715
Nat Genet. 2018 Jan;50(1):96-105
pubmed: 29203909
Nat Genet. 2014 Jan;46(1):17-23
pubmed: 24270360
Nat Plants. 2019 Aug;5(8):795-800
pubmed: 31332313
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Nature. 2011 Jan 20;469(7330):343-9
pubmed: 21248841
Genome Biol. 2017 Aug 31;18(1):163
pubmed: 28859663
Nature. 2020 Nov;587(7835):644-649
pubmed: 33057195
J Biol Chem. 2019 Feb 1;294(5):1451-1463
pubmed: 30514760
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17507-12
pubmed: 23045651
Nat Methods. 2019 Oct;16(10):999-1006
pubmed: 31501549
Nat Commun. 2017 Nov 21;8(1):1667
pubmed: 29162810
Nat Genet. 2011 Jun 05;43(7):715-9
pubmed: 21642989
Proc Natl Acad Sci U S A. 2010 May 11;107(19):8689-94
pubmed: 20395551
Angew Chem Int Ed Engl. 2019 Apr 1;58(15):4858-4862
pubmed: 30762296
Elife. 2013 Feb 26;2:e00348
pubmed: 23467541
Proc Natl Acad Sci U S A. 2020 Sep 22;117(38):23991-24000
pubmed: 32879011
Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3415-21
pubmed: 25092339
Nat Genet. 2016 Jun;48(6):694-9
pubmed: 27111035
Nat Genet. 2018 Oct;50(10):1452-1462
pubmed: 30224650
Nat Commun. 2019 Aug 13;10(1):3640
pubmed: 31409785
Curr Opin Plant Biol. 2019 Apr;48:36-46
pubmed: 31035031
Nat Commun. 2022 Mar 14;13(1):1335
pubmed: 35288562
Genome Biol. 2020 Jan 24;21(1):16
pubmed: 31973766
Mol Biol Evol. 2018 Aug 1;35(8):2060-2064
pubmed: 29860531
Annu Rev Plant Biol. 2015;66:243-67
pubmed: 25494460
Nucleic Acids Res. 2017 Jan 9;45(1):e4
pubmed: 27625391
Genome Biol. 2018 Feb 8;19(1):18
pubmed: 29422066
Proc Natl Acad Sci U S A. 2021 Feb 2;118(5):
pubmed: 33495321
Nat Plants. 2017 Sep;3(9):742-748
pubmed: 28848243
Nat Commun. 2020 May 27;11(1):2658
pubmed: 32461553
Nature. 2011 Dec 14;480(7378):490-5
pubmed: 22170606
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
BMC Biol. 2022 Mar 1;20(1):57
pubmed: 35227267
Genome Biol. 2015 Dec 01;16:259
pubmed: 26619908
Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8315-E8322
pubmed: 30104383
Science. 2021 Apr 9;372(6538):
pubmed: 33833093
Plant Physiol. 2016 Jul;171(3):2041-54
pubmed: 27208249
J Exp Bot. 2020 Aug 17;71(17):5119-5128
pubmed: 32374833
Trends Genet. 2019 Nov;35(11):818-827
pubmed: 31399242
Genome Res. 2017 Jul;27(7):1162-1173
pubmed: 28385710
Genome Biol. 2018 Jul 12;19(1):88
pubmed: 30001199
Plant J. 2020 Nov;104(3):596-612
pubmed: 32748498