Pan Yixuan, Liu Meiyang, Ruan Chun, Peng Mengyuan, Hao Min, Zhang Qi, Xue Jingdong, Niu Yanling, Li Ningzhe, Guan Haipeng, Wang Pei, Hu Mingqian, Li Haitao, Wang Wenjuan, Song Juan, Yao Yanhua, Lao Yimin, Li Bing
Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Department of Immunology and Microbiology, Shanghai Institute of Immunology and the Minister of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Nat Struct Mol Biol. 2025 Apr;32(4):687-697. doi: 10.1038/s41594-024-01453-w. Epub 2025 Jan 8.
The Rpd3S histone deacetylase complex has a crucial role in genomic integrity by deacetylating transcribed nucleosomes following RNA polymerase (Pol) II passage. Cryo-EM studies highlight the importance of asymmetrical Rco1-Eaf3 dimers in nucleosome binding, yet the interaction dynamics with nucleosomal substrates alongside elongating Pol II are poorly understood. Here we demonstrate the essential function of the Rco1 N-terminal intrinsically disordered region (IDR) in modulating Pol II association, in which K/R mutations within the Rco1 IDR impair interaction of Rpd3S with the C-terminal domain (CTD) of Rpb1, without affecting nucleosome recognition or complex integrity. We also identify the Rco1-PHD1 and Eaf3-CHD domains as crucial for specific binding to Ser5-phosphorylated CTD. The Rco1 IDR alleviates autoinhibition from its C terminus, facilitating PHD1-CHD engagement with phosphorylated CTD. Furthermore, we reveal a conserved mechanism by which asymmetrical Rco1-Eaf3 dimers coordinate nucleosome engagement and Pol II interaction, enhancing understanding of epigenetic complexes associated with transcriptional machinery.
Rpd3S组蛋白去乙酰化酶复合物通过在RNA聚合酶（Pol）II通过后使转录的核小体去乙酰化，在基因组完整性中发挥关键作用。冷冻电镜研究突出了不对称的Rco1-Eaf3二聚体在核小体结合中的重要性，但与沿延伸的Pol II的核小体底物的相互作用动力学仍知之甚少。在这里，我们证明了Rco1 N端内在无序区域（IDR）在调节Pol II结合中的基本功能，其中Rco1 IDR内的K/R突变损害了Rpd3S与Rpb1 C端结构域（CTD）的相互作用，而不影响核小体识别或复合物完整性。我们还确定Rco1-PHD1和Eaf3-CHD结构域对于特异性结合Ser5磷酸化的CTD至关重要。Rco1 IDR减轻了其C端的自抑制作用，促进了PHD1-CHD与磷酸化CTD的结合。此外，我们揭示了一种保守机制，通过该机制不对称的Rco1-Eaf3二聚体协调核小体结合和Pol II相互作用，增进了对与转录机制相关的表观遗传复合物的理解。
