H3K4 Methylation in ß-cells prevents transcriptional downregulation and variance associated with type 2 diabetes [ChIP-seq]

Insufficient insulin release by ß-cells is the primary etiology in type 2 diabetes (T2D) and coincides with impaired expression of genes essential to ß-cell function, but drivers of gene expression dysregulation are not well resolved. We find that H3K4me3 peak breadth correlates with gene expression dysregulation in T2D. Using an adult ß-cell Dpy30-KO mouse model, we show that global reduction of H3K4 methylation causes downregulation of genes also downregulated in T2D. Reduction of H3K4 methylation increases transcriptional entropy and reduces insulin production and glucose-responsiveness. Depletion of H3K4 methylation causes global dilution of epigenetic complexity but does not generally reduce gene expression – instead, genes related to ß-cell function and/or in particular chromatin environments are specifically affected. Our data further suggests that promoter-associated H3K4me1 is sufficient to maintain expression in the absence of H3K4me3. These data implicate dysregulation of H3K4 methylation in destabilizing gene expression and contributing to ß-cell dysfunction in T2D. Overall design: ChIP-seq for 4 histone modifications in 2 replicates from Dpy30-KO or CTRL mouse beta cells with 50% Drosophila S2 cell spike-in

β细胞胰岛素分泌不足是2型糖尿病（T2D）的主要病因，同时伴随β细胞功能必需基因的表达受损，但基因表达失调的驱动机制尚未得到充分阐明。我们发现，组蛋白H3赖氨酸4三甲基化（H3K4me3）峰宽与2型糖尿病中的基因表达失调存在相关性。利用成年β细胞Dpy30基因敲除（Dpy30-KO）小鼠模型，我们证实H3K4甲基化的整体水平降低会导致在2型糖尿病中同样出现表达下调的基因进一步下调。H3K4甲基化水平降低会增加转录熵，并降低胰岛素产生能力与葡萄糖应答性。H3K4甲基化的缺失会导致表观遗传复杂性的整体稀释，但并不会普遍降低基因表达；相反，与β细胞功能相关的基因，或处于特定染色质环境中的基因会受到特异性影响。我们的数据进一步表明，在缺乏H3K4me3的情况下，启动子相关的组蛋白H3赖氨酸4单甲基化（H3K4me1）足以维持基因表达。上述研究结果提示，H3K4甲基化失调会破坏基因表达稳定性，并参与2型糖尿病中β细胞功能异常的发生。
整体实验设计：在Dpy30-KO或对照（CTRL）小鼠胰岛β细胞中，针对4种组蛋白修饰开展染色质免疫共沉淀测序（ChIP-seq），设置2次生物学重复，并添加50%比例的果蝇S2细胞作为外参（spike-in）。