De novo methylation of nucleosomal DNA by the mammalian Dnmt1 and Dnmt3A DNA methyltransferases.
In the cell, DNA is wrapped on histone octamers, which reduces its accessibility for DNA interacting enzymes. We investigated de novo methylation of nucleosomal DNA in vitro and show that the Dnmt3a and Dnmt1 DNA methyltransferases efficiently methylate nucleosomal DNA without dissociation of the histone octamer from the DNA. In contrast, the prokaryotic SssI DNA methyltransferase and the catalytic domain of Dnmt3a are strongly inhibited by nucleosomes. We also found that full-length Dnmt1 and Dnmt3a bind to nucleosomes much stronger than their isolated catalytic domains, demonstrating that the N-terminal parts of the MTases are required for the interaction with nucleosomes. Variations of the DNA sequence or the histone tails did not significantly influence the methylation activity of Dnmt3a. The observation that mammalian methyltransferases directly modify nucleosomal DNA provides an insight into the mechanisms by which histone tail and DNA methylation patterns can influence each other because the DNA methylation pattern can be established while histones remain associated to the DNA.
Gowher
Humaira
H
School of Engineering and Science, International University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
Stockdale
Chris J
CJ
Goyal
Rachna
R
Ferreira
Helder
H
Owen-Hughes
Tom
T
Jeltsch
Albert
A
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002262:Carboxy-Lyases; D002384:Catalysis; D020134:Catalytic Domain; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000737:chemistry* / Q000378:metabolism; D019175:DNA Methylation; D000090205:DNA Methyltransferase 3A; D004268:DNA-Binding Proteins / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D051379:Mice; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated / Q000378:metabolism; D012097:Repressor Proteins / Q000378:metabolism; D014982:Xenopus laevis
D000076246:CCCTC-Binding Factor; C000619698:Ctcf protein, mouse; D004268:DNA-Binding Proteins; C000715535:Dnmt3a protein, mouse; C094335:H19 long non-coding RNA; D006657:Histones; D009707:Nucleosomes; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D012097:Repressor Proteins; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A; C000619381:Dnmt1 protein, mouse; D002262:Carboxy-Lyases; C022378:phosphoribosylaminoimidazole carboxylase