Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.
PLoS Genet. 2012 Sep;8(9):e1002952. doi: 10.1371/journal.pgen.1002952. Epub 2012 Sep 20.
Histone H3 di- and trimethylation on lysine 4 are major chromatin marks that correlate with active transcription. The influence of these modifications on transcription itself is, however, poorly understood. We have investigated the roles of H3K4 methylation in Saccharomyces cerevisiae by determining genome-wide expression-profiles of mutants in the Set1 complex, COMPASS, that lays down these marks. Loss of H3K4 trimethylation has virtually no effect on steady-state or dynamically-changing mRNA levels. Combined loss of H3K4 tri- and dimethylation results in steady-state mRNA upregulation and delays in the repression kinetics of specific groups of genes. COMPASS-repressed genes have distinct H3K4 methylation patterns, with enrichment of H3K4me3 at the 3'-end, indicating that repression is coupled to 3'-end antisense transcription. Further analyses reveal that repression is mediated by H3K4me3-dependent 3'-end antisense transcription in two ways. For a small group of genes including PHO84, repression is mediated by a previously reported trans-effect that requires the antisense transcript itself. For the majority of COMPASS-repressed genes, however, it is the process of 3'-end antisense transcription itself that is the important factor for repression. Strand-specific qPCR analyses of various mutants indicate that this more prevalent mechanism of COMPASS-mediated repression requires H3K4me3-dependent 3'-end antisense transcription to lay down H3K4me2, which seems to serve as the actual repressive mark. Removal of the 3'-end antisense promoter also results in derepression of sense transcription and renders sense transcription insensitive to the additional loss of SET1. The derepression observed in COMPASS mutants is mimicked by reduction of global histone H3 and H4 levels, suggesting that the H3K4me2 repressive effect is linked to establishment of a repressive chromatin structure. These results indicate that in S. cerevisiae, the non-redundant role of H3K4 methylation by Set1 is repression, achieved through promotion of 3'-end antisense transcription to achieve specific rather than global effects through two distinct mechanisms.
组蛋白 H3 赖氨酸 4 的二甲基化和三甲基化是与转录活性相关的主要染色质标记。然而，这些修饰对转录本身的影响知之甚少。我们通过确定 COMPASS（奠定这些标记的复合物）中 Set1 复合物的突变体的全基因组表达谱，研究了 H3K4 甲基化在酿酒酵母中的作用。H3K4 三甲基化的缺失几乎对稳态或动态变化的 mRNA 水平没有影响。H3K4 三甲基化和二甲基化的联合缺失导致稳态 mRNA 的上调，并延迟特定基因群的抑制动力学。COMPASS 抑制的基因具有独特的 H3K4 甲基化模式，在 3'-末端富集 H3K4me3，表明抑制与 3'-末端反义转录相关。进一步的分析表明，抑制是通过 H3K4me3 依赖性 3'-末端反义转录以两种方式介导的。对于一小部分基因，包括 PHO84，抑制是通过以前报道的需要反义转录本本身的反式效应介导的。然而，对于大多数 COMPASS 抑制的基因，反义转录本身的过程是抑制的重要因素。对各种突变体的特异性 qPCR 分析表明，这种更普遍的 COMPASS 介导的抑制机制需要 H3K4me3 依赖性 3'-末端反义转录来铺设 H3K4me2，这似乎是实际的抑制标记。3'-末端反义启动子的缺失也导致有义转录的去抑制，并使有义转录对 SET1 的额外缺失不敏感。在 COMPASS 突变体中观察到的去抑制作用类似于全局组蛋白 H3 和 H4 水平的降低，表明 H3K4me2 的抑制作用与建立抑制性染色质结构有关。这些结果表明，在酿酒酵母中，Set1 的 H3K4 甲基化的非冗余作用是抑制，通过促进 3'-末端反义转录来实现特定而非全局效应，通过两种不同的机制来实现。
