Conservation and divergence of methylation patterning in plants and animals.
Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.
Feng
Suhua
S
Howard Hughes Medical Institute, Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
Cokus
Shawn J
SJ
Zhang
Xiaoyu
X
Chen
Pao-Yang
PY
Bostick
Magnolia
M
Goll
Mary G
MG
Hetzel
Jonathan
J
Jain
Jayati
J
Strauss
Steven H
SH
Halpern
Marnie E
ME
Ukomadu
Chinweike
C
Sadler
Kirsten C
KC
Pradhan
Sriharsa
S
Pellegrini
Matteo
M
Jacobsen
Steven E
SE
D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D007438:Introns / Q000235:genetics; D009154:Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics; D015027:Zebrafish / Q000235:genetics; D029961:Zebrafish Proteins / Q000235:genetics
D015534:Trans-Activators; C517793:Uhrf1 protein, zebrafish; D029961:Zebrafish Proteins
Genome Res. 2002 Aug;12(8):1269-76
12176934
Nature. 2007 Dec 6;450(7171):908-12
17994007
Genetics. 2009 Jul;182(3):747-55
19433629
Curr Biol. 2007 Feb 20;17(4):379-84
17239600
Cell. 2008 May 2;133(3):523-36
18423832
Curr Biol. 2005 Jan 26;15(2):154-9
15668172
Nature. 2006 Oct 26;443(7114):931-49
17073008
Genes Dev. 2001 Oct 1;15(19):2585-97
11581163
Cell. 2006 Sep 22;126(6):1189-201
16949657
Science. 2002 Dec 13;298(5601):2157-67
12481130
Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5925-30
11983892
Nat Rev Genet. 2008 Jun;9(6):465-76
18463664
Science. 2009 Jun 12;324(5933):1451-4
19520962
Annu Rev Biochem. 2005;74:481-514
15952895
Mol Biol Evol. 2005 Apr;22(4):1119-28
15689527
Nat Struct Mol Biol. 2009 Sep;16(9):996-1001
19684599
Genome Res. 2004 Oct;14(10A):1861-9
15466286
Science. 2008 Mar 28;319(5871):1827-30
18339900
Science. 2006 Oct 27;314(5799):645-7
17068262
Science. 1999 Feb 19;283(5405):1164-7
10024242
PLoS Genet. 2008 Aug 15;4(8):e1000156
18704160
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
9862982
Nature. 2009 Nov 19;462(7271):315-22
19829295
Dev Biol. 2009 Oct 1;334(1):213-23
19631206
Nature. 2007 May 24;447(7143):418-24
17522675
Nat Struct Mol Biol. 2009 Sep;16(9):990-5
19684600
Genome Res. 2009 Oct;19(10):1732-41
19687145
Nature. 2008 Mar 13;452(7184):215-9
18278030
Genomics. 2007 Oct;90(4):530-41
17689048
J Biol Chem. 2002 Sep 13;277(37):34549-55
12084726
Science. 2010 May 14;328(5980):916-9
20395474
Genetics. 2004 Oct;168(2):809-16
15514055
Genome Res. 2007 May;17(5):625-31
17420183
Nature. 2008 Oct 9;455(7214):826-9
18772888
Bioessays. 2007 Mar;29(3):208-11
17295216
Nat Rev Genet. 2005 May;6(5):351-60
15861207
Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1570-5
17242348
Science. 2007 Sep 21;317(5845):1760-4
17673620