BACKGROUND DNA methylation is an epigenetic modification that mainly repress expression of genes essential during embryogenesis and development. There are key ATPase-dependent enzymes that read or write DNA methylation to remodel chromatin and regulate gene expression. Structural maintenance of chromosome hinge domain containing 1 (SMCHD1) is an architectural protein that regulates expression of numerous genes, some of which are imprinted, that are sensitive to DNA methylation. In addition, SMCHD1 germline mutations lead to developmental diseases; facioscapulohumoral muscular dystrophy (FSHD), bosma arhinia and micropthalmia (BAMS). Current evidence suggests that SMCHD1 functions through maintenance or de novo DNA methylation required for chromatin compaction. However, it is unclear if DNA methylation is also essential for genomic recruitment of SMCHD1 and its role as an architectural protein. We previously isolated SMCHD1 using a methylated DNA region from mouse pituitary growth hormone (Gh1) promoter, suggesting that methylation is required for SMCHD1 DNA binding. The goal of this study was to further understand DNA methylation directed role of SMCHD1 in regulating gene expression. Therefore, we profiled SMCHD1 genome wide occupancy in human neuroblastoma SH-SY5Y cells and evaluated if DNA methylation is required for SMCHD1 genomic binding by treating cells with the DNA demethylating reagent, 5-azacytidine (5-azaC). RESULTS Our data suggest that the majority of SMCHD1 binding occurs in intron and intergenic regions. Gene ontology analysis of genes associated with SMCHD1 genomic occupancy that is sensitive to 5-azaC treatment suggests SMCHD1 involvement in central nervous system development. The potassium voltage-gated channel subfamily Q member1 (KCNQ1) gene that associates with central nervous system is a known SMCHD1 target. We showed SMCHD1 binding to an intronic region of KCNQ1 that is lost following 5-azaC treatment suggesting DNA methylation facilitated binding of SMCHD1. Indeed, deletion of SMCHD1 by CRISPR- Cas9 increases KCNQ1 gene expression confirming its role in regulating KCNQ1 gene expression. CONCLUSION These findings provide novel insights on DNA methylation directed function of SMCHD1 in regulating expression of genes associated with central nervous system development that impact future drug development strategies.

中文翻译：

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DNA脱甲基试剂5-氮杂胞苷对SMCHD1基因组定位的影响。

背景技术DNA甲基化是一种表观遗传修饰，主要抑制胚胎发生和发育过程中必需基因的表达。有一些关键的ATPase依赖性酶可以读取或写入DNA甲基化，从而重塑染色质并调节基因表达。包含1的染色体铰链结构域（SMCHD1）的结构维护是一种结构蛋白，可调节众多对DNA甲基化敏感的基因的表达，其中一些基因已被印记。此外，SMCHD1种系突变会导致发育疾病。面肩肱型肌营养不良症（FSHD），bo性肌萎缩症和微眼睑炎（BAMS）。目前的证据表明，SMCHD1通过维持染色质压实所需的DNA甲基化或从头进行。然而，尚不清楚DNA甲基化是否对于SMCHD1的基因组募集及其作为建筑蛋白的作用是否也必不可少。我们以前使用来自小鼠垂体生长激素（Gh1）启动子的甲基化DNA区来分离SMCHD1，这表明SMCHD1 DNA结合需要甲基化。这项研究的目的是进一步了解SMCHD1在调节基因表达中的DNA甲基化指导作用。因此，我们分析了人类神经母细胞瘤SH-SY5Y细胞中SMCHD1基因组范围的占用情况，并通过用DNA脱甲基试剂5-azacytidine（5-azaC）处理细胞来评估SMCHD1基因组结合是否需要DNA甲基化。结果我们的数据表明大多数SMCHD1结合发生在内含子和基因间区域。对5-azaC治疗敏感的SMCHD1基因组占用相关基因的基因本体分析表明，SMCHD1参与中枢神经系统发育。与中枢神经系统相关的钾电压门控通道亚家族Q成员1（KCNQ1）基因是已知的SMCHD1目标。我们显示SMCHD1绑定到KCNQ1的内含子区域，该区域在5-azaC处理后丢失，这表明DNA甲基化促进了SMCHD1的结合。实际上，通过CRISPR-Cas9删除SMCHD1增加了KCNQ1基因表达，证实了其在调节KCNQ1基因表达中的作用。结论这些发现为SMCHD1的DNA甲基化指导功能在调节与中枢神经系统发育相关的基因表达（影响未来药物开发策略）中的功能提供了新颖的见解。