Kim Sang-Ah, Chatterjee Nilanjana, Jennings Matthew J, Bartholomew Blaine, Tan Song
Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, 108 Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802-1014, USA.
UT MD Anderson Cancer Center, Department of Epigenetics and Molecular Carcinogenesis, 1808 Park Road 1C, Smithville, TX 78957, USA.
Nucleic Acids Res. 2015 May 26;43(10):4868-80. doi: 10.1093/nar/gkv388. Epub 2015 Apr 27.
The promoter regions of active genes in the eukaryotic genome typically contain nucleosomes post-translationally modified with a trimethyl mark on histone H3 lysine 4 (H3K4), while transcriptional enhancers are marked with monomethylated H3K4. The flavin-dependent monoamine oxidase LSD1 (lysine-specific demethylase 1, also known as KDM1) demethylates mono- and dimethylated H3K4 in peptide substrates, but requires the corepressor protein, CoREST, to demethylate nucleosome substrates. The molecular basis for how the LSD1/CoREST complex interacts with its physiological nucleosome substrate remains largely unknown. We examine here the role of extranucleosomal DNA beyond the nucleosome core particle for LSD1/CoREST function. Our studies of LSD1/CoREST's enzyme activity and nucleosome binding show that extranucleosomal DNA dramatically enhances the activity of LSD1/CoREST, and that LSD1/CoREST binds to the nucleosome as a 1:1 complex. Our photocrosslinking experiments further indicate both LSD1 and CoREST subunits are in close contact with DNA around the nucleosome dyad as well as extranucleosomal DNA. Our results suggest that the LSD1/CoREST interacts with extranucleosomal DNA when it productively engages its nucleosome substrate.
真核生物基因组中活跃基因的启动子区域通常含有在组蛋白H3赖氨酸4（H3K4）上经翻译后修饰带有三甲基标记的核小体，而转录增强子则带有单甲基化的H3K4。黄素依赖性单胺氧化酶LSD1（赖氨酸特异性去甲基化酶1，也称为KDM1）可使肽底物中的单甲基化和二甲基化H3K4去甲基化，但需要共抑制蛋白CoREST才能使核小体底物去甲基化。LSD1/CoREST复合物如何与其生理性核小体底物相互作用的分子基础在很大程度上仍然未知。我们在此研究核小体核心颗粒之外的核小体外DNA对LSD1/CoREST功能的作用。我们对LSD1/CoREST的酶活性和核小体结合的研究表明，核小体外DNA显著增强了LSD1/CoREST的活性，并且LSD1/CoREST以1:1复合物的形式与核小体结合。我们的光交联实验进一步表明，LSD1和CoREST亚基都与核小体二分体周围的DNA以及核小体外DNA紧密接触。我们的结果表明，LSD1/CoREST在有效结合其核小体底物时会与核小体外DNA相互作用。
