Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
JST-ERATO, Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Sci Rep. 2018 Feb 8;8(1):2656. doi: 10.1038/s41598-018-21060-2.
Chromatin structure and gene expression are dynamically regulated by posttranslational modifications of histones. Recent advance in mass spectrometry has identified novel types of lysine acylations, such as butyrylation and malonylation, whose functions and regulations are likely different from those of acetylation. Sirtuins, nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylases, catalyze various deacylations. However, it is poorly understood how distinct sirtuins regulate the histone acylation states of nucleosomes that have many lysine residues. Here, we provide mass spectrometry-based quantitative information about the acyl group- and site-selectivity of all human sirtuins on acylated nucleosomes. The acyl group- and site-selectivity of each sirtuin is unique to its subtype. Sirt5 exclusively removes negatively-charged acyl groups, while Sirt1/2/3/6/7 preferentially remove hydrophobic acyl groups; Sirt1 and Sirt3 selectively remove acetyl group more than butyryl group, whereas Sirt2 and Sirt6 showed the opposite selectivity. Investigating site-selectivity for active sirtuins revealed acylated lysines on H4 tails to be poor substrates and acylated H3K18 to be a good substrate. Furthermore, we found Sirt7 to be a robust deacylase of H3K36/37, and its activity reliant on nucleosome-binding at its C-terminal basic region. All together, our quantitative dataset provides a useful resource in understanding chromatin regulations by histone acylations.
染色质结构和基因表达是通过组蛋白的翻译后修饰动态调控的。质谱技术的最新进展鉴定了新型赖氨酸酰化类型，如丁酰化和丙二酰化，其功能和调控可能与乙酰化不同。Sirtuins 是烟酰胺腺嘌呤二核苷酸（NAD）依赖性组蛋白去乙酰化酶，可催化多种脱酰反应。然而，不同的 Sirtuins 如何调节具有许多赖氨酸残基的核小体的组蛋白酰化状态仍知之甚少。在这里，我们提供了基于质谱的关于所有人类 Sirtuins 在酰化核小体上的酰基和位点选择性的定量信息。每种 Sirtuin 的酰基和位点选择性与其亚型特异性相关。Sirt5 专门去除带负电荷的酰基，而 Sirt1/2/3/6/7 优先去除疏水性酰基；Sirt1 和 Sirt3 选择性去除乙酰基多于丁酰基，而 Sirt2 和 Sirt6 则表现出相反的选择性。对活性 Sirtuins 的位点选择性研究表明，H4 尾部的酰化赖氨酸是较差的底物，而 H3K18 的酰化是较好的底物。此外，我们发现 Sirt7 是 H3K36/37 的强有力的脱酰酶，其活性依赖于其 C 末端碱性区域与核小体的结合。总的来说，我们的定量数据集为理解组蛋白酰化对染色质调控提供了有用的资源。
