Regulation of chromatin structure by Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase [histone turnover]. Saccharomyces cerevisiae

Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylation−demethylation control chromatin dynamics during various facets of transcriptional regulation. Overall design: Genome-wide nucleosome maps were generated from three different yeast strains representing no tag control, 8V5-Set1 and Jhd2-12V5. Cells were cross-linked with formaldehyde, spheroplasted, nuclei were isolated and chromatin was prepared using micrococcal nuclease digestion, chromatin immunoprecipitation was performed using an epitope-tag specific antibody, libraries were prepared from ChIP and input DNA, sequenced, and analyzed separately.

组蛋白H3K4甲基化（Histone H3K4 methylation）在从酵母到人类的物种中均与基因转录密切相关，但其在转录与染色质动态变化中的机制性作用仍不甚明晰。本研究以酿酒酵母（Saccharomyces cerevisiae，S. cerevisiae）为模型，探究了唯一的H3K4甲基转移酶Set1与唯一的H3K4去甲基化酶Jhd2的功能。研究数据显示，Set1与Jhd2主要通过协同方式调控基因转录。我们发现，二者通过H3K4甲基化的协同活性，可对共有靶基因的转录分别发挥正向或负向调控作用。从机制层面来看，本研究数据揭示，在转录协同调控过程中，Set1与Jhd2共同调控核小体占据情况。此外，我们还观察到，在酿酒酵母不同转录活跃/非活跃基因组别以及基因内部的不同区域中，Set1与Jhd2可对核小体及染色质结构进行全基因组范围的显著协同调控。综上，本研究提出了一个调控模型：Set1与Jhd2通过H3K4甲基化-去甲基化的协同作用，在转录调控的多个环节中调控染色质动态变化。

总体实验设计：本研究从三类不同酿酒酵母菌株中制备全基因组核小体图谱，分别为无标签对照菌株、8V5-Set1菌株与Jhd2-12V5菌株。具体实验流程如下：用甲醛对细胞进行交联，制备原生质体，分离细胞核后采用微球菌核酸酶消化制备染色质；使用表位标签特异性抗体开展染色质免疫沉淀（ChIP）实验；分别从ChIP产物与输入DNA中构建测序文库，完成测序后进行独立数据分析。