School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel.
PLoS Biol. 2012;10(7):e1001369. doi: 10.1371/journal.pbio.1001369. Epub 2012 Jul 31.
Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. We therefore have systematically investigated the effects of 83 histone mutants, and 119 gene deletion mutants, on induction/repression dynamics of 170 transcripts in response to diamide stress in yeast. Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. Furthermore, by jointly analyzing the substrates (histone mutants) and enzymes (chromatin modifier deletions) we identify specific interactions between histone modifications and their regulators. Combining these functional results with genome-wide mapping of several histone marks in the same time course, we systematically investigated the correspondence between histone modification occurrence and function. We followed up on one pathway, finding that Set1-dependent H3K4 methylation primarily acts as a gene repressor during multiple stresses, specifically at genes involved in ribosome biosynthesis. Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and identify a significant role for the "activating" mark H3K4me3 in gene repression.
真核基因组包装成染色质对基因转录有广泛的影响。奇怪的是，人们通常观察到，删除一个全局染色质调节剂只会影响到与被研究的调节剂结合或修饰的有限数量的基因的表达。然而，在许多单基因研究中已经清楚地表明，染色质调节剂通常不会影响稳态转录，而是需要通过环境线索来进行正常的转录重编程。因此，我们系统地研究了 83 种组蛋白突变体和 119 种基因缺失突变体对酵母中 170 个转录物在二酰胺应激下的诱导/抑制动力学的影响。重要的是，我们发现染色质调节剂在基因诱导/抑制过程中发挥的作用远比在稳态表达中更为显著。此外，通过联合分析底物（组蛋白突变体）和酶（染色质修饰物缺失），我们确定了组蛋白修饰与其调节剂之间的特定相互作用。将这些功能结果与同一时间过程中几个组蛋白标记的全基因组作图相结合，我们系统地研究了组蛋白修饰发生与功能之间的对应关系。我们对一条途径进行了跟进，发现 Set1 依赖性 H3K4 甲基化主要在多种应激下作为基因抑制剂起作用，特别是在参与核糖体生物合成的基因上。Set1 依赖性核糖体基因抑制作用是通过核糖体蛋白基因和核糖体生物发生基因的不同途径发生的，可以根据抑制的遗传要求以及在基因抑制过程中染色质的变化来区分这些途径。总之，我们的动态研究为研究染色质调控提供了丰富的资源，并确定了“激活”标记 H3K4me3 在基因抑制中的重要作用。
