Abeywardana Tharindumala, Wu Xiwei, Huang Shih-Ting, Aldana Masangkay Grace, Rodin Andrei S, Branciamore Sergio, Gogoshin Grigoriy, Li Arthur, Du Li, Tharuka Neranjan, Tomaino Ross, Chen Yuan
University of California, San Diego.
Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope.
Res Sq. 2024 Apr 2:rs.3.rs-4201913. doi: 10.21203/rs.3.rs-4201913/v1.
Enhancers are fundamental to gene regulation. Post-translational modifications by the small ubiquitin-like modifiers (SUMO) modify chromatin regulation enzymes, including histone acetylases and deacetylases. However, it remains unclear whether SUMOylation regulates enhancer marks, acetylation at the 27th lysine residue of the histone H3 protein (H3K27Ac). To investigate whether SUMOylation regulates H3K27Ac, we performed genome-wide ChIP-seq analyses and discovered that knockdown (KD) of the SUMO activating enzyme catalytic subunit UBA2 reduced H3K27Ac at most enhancers. Bioinformatic analysis revealed that TFAP2C-binding sites are enriched in enhancers whose H3K27Ac was reduced by UBA2 KD. ChIP-seq analysis in combination with molecular biological methods showed that TFAP2C binding to enhancers increased upon UBA2 KD or inhibition of SUMOylation by a small molecule SUMOylation inhibitor. However, this is not due to the SUMOylation of TFAP2C itself. Proteomics analysis of TFAP2C interactome on the chromatin identified histone deacetylation (HDAC) and RNA splicing machineries that contain many SUMOylation targets. TFAP2C KD reduced HDAC1 binding to chromatin and increased H3K27Ac marks at enhancer regions, suggesting that TFAP2C is important in recruiting HDAC machinery. Taken together, our findings provide insights into the regulation of enhancer marks by SUMOylation and TFAP2C and suggest that SUMOylation of proteins in the HDAC machinery regulates their recruitments to enhancers.
增强子对于基因调控至关重要。小泛素样修饰物（SUMO）的翻译后修饰可修饰染色质调控酶，包括组蛋白乙酰转移酶和去乙酰化酶。然而，SUMO化是否调节增强子标记，即组蛋白H3蛋白第27位赖氨酸残基处的乙酰化（H3K27Ac），仍不清楚。为了研究SUMO化是否调节H3K27Ac，我们进行了全基因组ChIP-seq分析，发现SUMO激活酶催化亚基UBA2的敲低（KD）降低了大多数增强子处的H3K27Ac。生物信息学分析表明，TFAP2C结合位点在其H3K27Ac被UBA2 KD降低的增强子中富集。ChIP-seq分析结合分子生物学方法表明，在UBA2 KD或小分子SUMO化抑制剂抑制SUMO化后，TFAP2C与增强子的结合增加。然而，这并非由于TFAP2C自身的SUMO化。对染色质上TFAP2C相互作用组的蛋白质组学分析鉴定出了包含许多SUMO化靶点的组蛋白去乙酰化（HDAC）和RNA剪接机制。TFAP2C KD减少了HDAC1与染色质的结合，并增加了增强子区域的H3K27Ac标记，表明TFAP2C在招募HDAC机制中很重要。综上所述，我们的研究结果为SUMO化和TFAP2C对增强子标记的调控提供了见解，并表明HDAC机制中蛋白质的SUMO化调节了它们向增强子的募集。
