Physical and functional interaction between the SET1/COMPASS complex component CFP-1/CXXC and a Sin3S HDAC complex

The CFP1/CXXC protein targets SET1/COMPASS complexes to non-methylated CpG rich promoter regions to implement tri-methylation of histone H3 Ly4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss depend on chromatin context. Little is known about how CFP1 binding is coordinated with other chromatin factors. Using a proteomics approach, we establish a link between C. elegans CFP1 and a small Rpd3/Sin3 histone deacetylase (HDAC) complex (Sin3S). Mutants of CFP-1, SIN-3, and the catalytic subunit SET-2/SET1 have similar phenotypes and misregulate the expression of common genes. CFP-1 directly interacts with SIN-3 through a region including the conserved PAH1 domain, and contributes to recruitment of SIN-3 and the Sin3S subunit HDA-1 to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3 HDAC small complex at promoters, with implications for the coordinate regulation of gene expression by chromatin- associated complexes with distinct activities. ChIP-seq was used to profile H3K4me3, SIN-3, and HDA-1 in wild-type, cfp-1, and set-2 mutant C. elegans embryos

CFP1/CXXC蛋白可将SET1/COMPASS复合物靶向至未甲基化CpG富集的启动子区域，介导组蛋白H3赖氨酸4的三甲基化（H3K4me3）。尽管H3K4me3广泛与基因表达相关，但CFP1缺失所产生的效应取决于染色质的局部上下文环境。目前学界对CFP1的结合如何与其他染色质因子协同调控的机制仍知之甚少。
本研究通过蛋白质组学方法，确立了秀丽隐杆线虫（C. elegans）CFP1与小型Rpd3/Sin3组蛋白去乙酰化酶（histone deacetylase, HDAC）复合物（Sin3S）之间的关联。CFP-1、SIN-3以及催化亚基SET-2/SET1的突变体具有相似的表型，并异常调控了一批共有基因的表达。
CFP-1可通过包含保守PAH1结构域的区域与SIN-3直接相互作用，并协助将SIN-3及Sin3S亚基HDA-1招募至富集H3K4me3的启动子区域。
本研究结果揭示了CFP-1在介导SET1/COMPASS复合物与小型Sin3 HDAC复合物在启动子区域相互作用中的全新功能，为具有不同活性的染色质相关复合物协同调控基因表达提供了新的启示。本研究采用染色质免疫共沉淀测序（ChIP-seq）技术，对野生型、cfp-1突变型及set-2突变型秀丽隐杆线虫胚胎中的H3K4me3、SIN-3及HDA-1进行了谱图分析。