Takeshima Hideyuki, Suetake Isao, Tajima Shoji
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
J Mol Biol. 2008 Nov 21;383(4):810-21. doi: 10.1016/j.jmb.2008.03.001. Epub 2008 Mar 8.
In mammals, DNA methylation is crucial for embryonic development and germ cell differentiation. The DNA methylation patterns are created by de novo-type DNA methyltransferases (Dnmts) 3a and 3b. Dnmt3a is crucial for global methylation, including that of imprinted genes in germ cells. In eukaryotic nuclei, genomic DNA is packaged into multinucleosomes with linker histone H1, which binds to core nucleosomes, simultaneously making contacts in the linker DNA that separates adjacent nucleosomes. In the present study, we prepared oligonucleosomes from HeLa nuclei with or without linker histone H1 and used them as a substrate for Dnmt3a. Removal of histone H1 enhanced the DNA methylation activity. Furthermore, Dnmt3a preferentially methylated the linker between the two nucleosome core regions of reconstituted dinucleosomes, and the binding of histone H1 inhibited the DNA methylation activity of Dnmt3a towards the linker DNA. Since an identical amount of histone H1 did not inhibit the activity towards naked DNA, the inhibitory effect of histone H1 was not on the Dnmt3a catalytic activity but on its preferential location in the linker DNA of the dinucleosomes. The central globular domain and C-terminal tail of the histone H1 molecule were indispensable for inhibition of the DNA methylation activity of Dnmt3a. We propose that the binding and release of histone H1 from the linker portion of chromatin may regulate the local DNA methylation of the genome by Dnmt3a, which is expressed ubiquitously in somatic cells in vivo.
在哺乳动物中，DNA甲基化对于胚胎发育和生殖细胞分化至关重要。DNA甲基化模式由从头型DNA甲基转移酶（Dnmts）3a和3b产生。Dnmt3a对于全局甲基化至关重要，包括生殖细胞中印迹基因的甲基化。在真核细胞核中，基因组DNA与连接组蛋白H1一起包装成多核小体，连接组蛋白H1与核心核小体结合，同时在分隔相邻核小体的连接DNA中形成接触。在本研究中，我们从含有或不含有连接组蛋白H1的HeLa细胞核中制备了寡核小体，并将它们用作Dnmt3a的底物。去除组蛋白H1增强了DNA甲基化活性。此外，Dnmt3a优先甲基化重组双核小体的两个核小体核心区域之间的连接区，并且组蛋白H1的结合抑制了Dnmt3a对连接DNA的甲基化活性。由于相同量的组蛋白H1不抑制对裸露DNA的活性，组蛋白H1的抑制作用不是针对Dnmt3a催化活性而是针对其在双核小体连接DNA中的优先定位。组蛋白H1分子的中央球状结构域和C末端尾巴对于抑制Dnmt3a的DNA甲基化活性是必不可少的。我们提出组蛋白H1从染色质连接部分的结合和释放可能通过Dnmt3a调节基因组的局部DNA甲基化，Dnmt3a在体内体细胞中普遍表达。
