Leo1 and Set1-mediated H3K4me3 contribute to sterol homeostasis in yeast [RNA-seq]

Project Abstract : Trimethylation of histone H3 lysine 4 (H3K4me3) is predominantly associated with transcriptional start sites (TSSs) and is believed to facilitate transcription initiation. Furthermore, H3K4me3 plays a role in defining cell fate and specific cellular functions. Nevertheless, the precise function of H3K4me3 in transcription activation remains a topic of ongoing debate. The Polymerase-associated factor 1 complex (Paf1C), which is integral to various transcription-related cellular processes, consists of five highly conserved subunits: Paf1, Ctr9, Rtf1, Cdc73, and Leo1. While all subunits of Paf1C are indispensable for the maintenance of H3K4 methylation levels, it is noteworthy that strains lacking Leo1 exhibited unaltered levels of H3K4me3. To elucidate the role of H3K4me3, we conducted a transcriptome analysis coupled with ChIP-sequencing of H3K4me3 in cells lacking Leo1. Our research uncovers a distinctive role of Leo1 in yeast, whereby it plays a pivotal role in maintaining sterol homeostasis through the suppression of Upc2 expression. Importantly, this role stands apart from the functions of other Paf1C subunits. H3K4me3 is essential for promoting the expression of sterol uptake genes that are Upc2-dependent when Leo1 is absent. Additionally, Set1 contributes to sterol homeostasis by regulating iron metabolism and mitochondrial functions rather than directly suppressing Upc2 expression. Therefore, our findings reveal a novel role for Leo1 in sterol homeostasis and highlight the importance of H3K4me3 in promoting transcription of response genes required for sterol uptake.项目摘要：组蛋白H3赖氨酸4三甲基化（H3K4me3）主要富集于转录起始位点（TSSs），被认为可促进转录起始过程。此外，H3K4me3在细胞命运决定及特定细胞功能维持中发挥关键作用。然而，其在转录激活中的精确功能仍存在持续争议。聚合酶相关因子1复合物（Paf1C）广泛参与各类转录相关细胞过程，由Paf1、Ctr9、Rtf1、Cdc73与Leo1五个高度保守的亚基构成。尽管Paf1C的所有亚基均为维持H3K4甲基化水平所必需，但值得注意的是，缺失Leo1的细胞其H3K4me3水平并未发生改变。为阐明H3K4me3的功能机制，本研究对缺失Leo1的酵母细胞开展了转录组分析及H3K4me3染色质免疫共沉淀测序（ChIP-seq）。研究结果显示，Leo1在酵母中具有独特功能：其通过抑制Upc2基因表达，在维持固醇稳态中扮演核心角色，且该功能独立于Paf1C其他亚基的功能。在Leo1缺失的背景下，H3K4me3对于促进Upc2依赖型固醇摄取基因的表达至关重要。此外，Set1蛋白通过调控铁代谢与线粒体功能参与固醇稳态维持，而非直接抑制Upc2基因表达。综上，本研究揭示了Leo1在固醇稳态调控中的全新功能，并凸显了H3K4me3在介导固醇摄取相关应答基因转录中的重要意义。