Genome-wide mapping of H3K4me1 status in primary adipocytes isolated from wild-type (WT) and Lonp1-knockout (LONP1 AKO) mice

Mitochondrial proteases are emerging as key regulators of mitochondrial plasticity acting both as protein quality surveillance and regulatory enzymes by performing highly regulated proteolytic reactions. It remains unclear, however, whether the regulated mitochondrial proteolysis is mechanistically linked to cell identity switch such as white-to-beige conversion of adipocytes. We found that disruption of LONP1-dependent proteolysis substantially impairs thermogenic molecular program and cellular respiration in in vitro differentiated primary adipocytes. qPCR analysis showed that expression levels of Ucp1 and other beige adipocyte thermogenic genes were remarkably downregulated in LONP1 AKO adipocytes. We took a deeper dive into the characterization of histone modifications in LONP1 AKO adipocytes using the global enhancer marker H3K4me1 ChIP-Seq. These unbiased ChIP seq data are strong evidence of that LONP1 loss results in decreased H3K4me1 on a broad array of thermogenic genes. These results collectively indicate that LONP1 is crucial to maintain proper epigenetic homeostasis and beige thermogenic gene expression. Overall design: Using genome-wide approach, ChIPseq, to delineate active enhancer hallmark H3K4me1 on LONP1-dependent beige thermogenic genes

线粒体蛋白酶（mitochondrial proteases）正逐渐成为线粒体可塑性（mitochondrial plasticity）的关键调控因子，其通过介导高度受控的蛋白水解反应，同时兼具蛋白质质量监测（protein quality surveillance）与调控酶（regulatory enzymes）的功能。
然而目前尚不清楚，受调控的线粒体蛋白水解（regulated mitochondrial proteolysis）是否与细胞身份转换（cell identity switch）存在机制层面的关联，例如脂肪细胞的白色向米色转化（white-to-beige conversion of adipocytes）。
本研究发现，靶向破坏LONP1依赖的蛋白水解（LONP1-dependent proteolysis）过程，会显著损害体外分化原代脂肪细胞（in vitro differentiated primary adipocytes）中的产热分子程序（thermogenic molecular program）与细胞呼吸（cellular respiration）功能。
定量聚合酶链反应（qPCR）分析显示，在LONP1脂肪细胞特异性敲除（LONP1 AKO）脂肪细胞中，解偶联蛋白1（Ucp1）及其他米色脂肪细胞产热基因（beige adipocyte thermogenic genes）的表达水平显著下调。
我们借助全局增强子标记物组蛋白H3赖氨酸4单甲基化（H3K4me1）染色质免疫共沉淀测序（ChIP-Seq），对LONP1 AKO脂肪细胞中的组蛋白修饰（histone modifications）开展了更为深入的表征分析。
这些无偏倚的ChIP-Seq数据有力证明，LONP1的缺失会导致大量产热基因上的H3K4me1水平显著降低。
上述研究结果共同表明，LONP1对于维持正常的表观遗传稳态（epigenetic homeostasis）以及米色脂肪细胞产热基因的表达至关重要。
整体实验设计：采用全基因组方法（genome-wide approach）结合染色质免疫共沉淀测序（ChIP-Seq），解析LONP1依赖的米色产热基因上的活性增强子标志性修饰（active enhancer hallmark）H3K4me1。