Determinants of H3K4me pattern establishment. Saccharomyces cerevisiae

A hallmark of genes transcribed by RNA polymerase II (RNApII) is a "gradient" of histone H3 lysine 4 (H3K4) methylation. Various factors differentially bind to H3K4me3 near promoters, H3K4me2 just downstream, and H3K4me1 further downstream to modulate gene expression. Set1/COMPASS, the single S. cerevisiae H3K4 methyltransferase, binds transcribing RNApII, but COMPASS may also be allosterically regulated by specific subunits and histone H2B ubiquitylation. To ask whether differential H3K4 methylation is determined by regulated activity at specific gene locations or by the amount of time COMPASS spends near the nucleosome, ChIP-Seq analyses was performed in cells with altered transcription elongation rates or with Set1 fused to RNApII. Our results support a simple model where higher H3K4 methylations result from both increased duration and frequency of COMPASS proximity to the nucleosome. Overall design: 99 Samples of H3K4me3, H3K4me2, H3K4me1, H3, RPB3, RPB4, Ser5 and Ser2 ChIP-Seq for S.cerevisiae in wild type and relevant mutant conditions.

由RNA聚合酶II（RNA polymerase II）转录的基因的标志性特征之一，是组蛋白H3赖氨酸4（histone H3 lysine 4）甲基化的梯度分布。多种因子可差异化结合启动子附近的H3K4三甲基化（H3K4me3）、转录起始位点下游的H3K4二甲基化（H3K4me2），以及更下游的H3K4单甲基化（H3K4me1），从而调控基因表达。酿酒酵母（S. cerevisiae）中唯一的H3K4甲基转移酶Set1/COMPASS复合物可结合正在转录的RNA聚合酶II，但该复合物也可通过特定亚基与组蛋白H2B泛素化实现变构调控。为明确差异化的H3K4甲基化究竟由特定基因位点的调控活性决定，还是由COMPASS靠近核小体的时长决定，我们对转录延伸速率发生改变的细胞，或是将Set1融合至RNA聚合酶II的细胞开展了染色质免疫共沉淀测序（ChIP-Seq）分析。本研究结果支持一个简洁模型：更高水平的H3K4甲基化源于COMPASS靠近核小体的时长与频率同时增加。整体实验设计：针对酿酒酵母（S. cerevisiae）的野生型与相关突变株条件，共设置99个ChIP-Seq样本，检测靶点涵盖H3K4me3、H3K4me2、H3K4me1、总组蛋白H3、RPB3、RPB4、Ser5及Ser2。