Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia.
Institute of Gene Biology RAS, 119071 Moscow, Russia.
Int J Mol Sci. 2021 Jul 15;22(14):7587. doi: 10.3390/ijms22147587.
Gain and loss of DNA methylation in cells is a dynamic process that tends to achieve an equilibrium. Many factors are involved in maintaining the balance between DNA methylation and demethylation. Previously, it was shown that methyl-DNA protein Kaiso may attract NCoR, SMRT repressive complexes affecting histone modifications. On the other hand, the deficiency of Kaiso resulted in reduced methylation of ICR in locus and promoter in mouse embryonic fibroblasts. However, nothing is known about how Kaiso influences DNA methylation at the genome level. Here we show that deficiency of Kaiso led to whole-genome hypermethylation, using Kaiso deficient human renal cancer cell line obtained via CRISPR/CAS9 genome editing. However, Kaiso serves to protect genic regions, enhancers, and regions with a low level of histone modifications from demethylation. We detected hypomethylation of binding sites for Oct4 and Nanog in Kaiso deficient cells. Kaiso immunoprecipitated with de novo DNA methyltransferases DNMT3a/3b, but not with maintenance methyltransferase DNMT1. Thus, Kaiso may attract methyltransferases to surrounding regions and modulate genome methylation in renal cancer cells apart from being methyl DNA binding protein.
细胞中 DNA 甲基化的获得和丢失是一个趋向于达到平衡的动态过程。许多因素参与维持 DNA 甲基化和去甲基化之间的平衡。先前已经表明，甲基化 DNA 蛋白 Kaiso 可能会吸引 NCoR、SMRT 抑制复合物，影响组蛋白修饰。另一方面，Kaiso 的缺乏导致小鼠胚胎成纤维细胞中 ICR 位点和 启动子的甲基化减少。然而，目前尚不清楚 Kaiso 如何影响基因组水平的 DNA 甲基化。在这里，我们使用通过 CRISPR/CAS9 基因组编辑获得的 Kaiso 缺陷型人肾癌细胞系，表明 Kaiso 缺乏会导致全基因组超甲基化。然而，Kaiso 有助于保护基因区域、增强子和组蛋白修饰水平低的区域免受去甲基化。我们在 Kaiso 缺陷型细胞中检测到 Oct4 和 Nanog 结合位点的低甲基化。Kaiso 与从头甲基转移酶 DNMT3a/3b 免疫沉淀，而不是与维持甲基转移酶 DNMT1 免疫沉淀。因此，Kaiso 可能会吸引甲基转移酶到周围区域，并调节肾癌细胞中的基因组甲基化，而不仅仅是作为甲基化 DNA 结合蛋白。
