Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved insulin secretion by pancreatic beta cells

Aging at the cellular level is driven by changes in gene activity and epigenetic state that are only partially understood. We performed a comprehensive epigenomic analysis of the pancreatic beta cell, key player in glucose homeostasis and diabetes, in adolescent and very old mice. Globally, we observe a general methylation drift resulting in an overall more leveled methylome, suggesting that the maintenance of highly differential methylation patterns becomes compromised with advanced age. Importantly, we discover targeted changes in the methylation status of beta cell proliferation and function genes that go against the global methylation drift, are specific to beta cells, and correlate with repression of the proliferation program and activation of metabolic regulators. These targeted alterations frequently occur at distal cis-regulator elements, and are associated with specific chromatin marks and transcription factor occupancy in young beta cells. Strikingly, we find the insulin secretory response to glucose much improved in mature beta cells in mice, as predicted by the changes in methylome and transcriptome and in contrast to the decline in function observed in aged human beta cells. Thus, aging of terminally differentiated cells in mammals is not always coupled to functional decline. RNA-seq was done on 3 biological replicas from old and three from young beta cells. each sample originated from a pool of 5-10 mic.e H3K27me3 ChIP-seq was done with two replicas for old mice (pool of 4-7 mice) and the rest of the ChIPseq (H3K4me1, H3K27ac and young H3K27me3) was sone with one sample (pool of few mice). BIS-seq was done on one sample from a pool of 10 young mice and one sample of a pool of old mice (18-22 months old)细胞水平的衰老由基因活性与表观遗传状态的改变所驱动，而这些改变的机制目前仅被部分阐明。我们针对青春期及极老龄小鼠的胰腺β细胞（pancreatic beta cell）开展了全面的表观基因组学分析——该细胞是维持葡萄糖稳态与参与糖尿病发病的关键细胞类型。整体而言，我们观察到普遍的甲基化漂移现象，使得整体甲基化组（methylome）趋于均一化，这提示随着年龄增长，高度差异化甲基化模式的维持能力会出现受损。尤为重要的是，我们发现了一批靶向性的甲基化状态改变：这些改变发生于β细胞增殖与功能相关基因，与整体甲基化漂移趋势相悖，且仅特异性存在于β细胞中，同时与增殖程序的抑制以及代谢调控因子的激活呈现相关性。这类靶向性改变常发生于远端顺式调控元件（distal cis-regulatory elements），且与年轻β细胞中特定的染色质修饰标记及转录因子结合占据特征相关联。令人瞩目的是，正如甲基化组与转录组（transcriptome）的改变所预测的那样，我们发现小鼠成熟β细胞对葡萄糖的胰岛素分泌响应能力显著提升，这与衰老人类β细胞的功能衰退现象形成鲜明对比。由此可见，哺乳动物终末分化细胞的衰老并不总是伴随功能衰退。RNA-seq实验共使用3份老龄小鼠β细胞生物学重复样本与3份年轻小鼠β细胞生物学重复样本，每份样本均来自5-10只小鼠的混合组织。H3K27me3染色质免疫沉淀测序（ChIP-seq, chromatin immunoprecipitation sequencing）针对老龄小鼠设置了2份生物学重复，每份样本来自4-7只小鼠的混合组织；其余ChIP-seq实验（涵盖H3K4me1、H3K27ac及年轻小鼠的H3K27me3）仅使用1份混合样本（来自少量小鼠）。亚硫酸氢盐测序（BIS-seq）共设置2份样本：1份来自10只年轻小鼠的混合组织，另1份来自18-22月龄的老龄小鼠混合组织。