Chromatin dynamics in yeast

真核生物基因组包装入染色质影响DNA模板化过程 从转录到重组，但我们仍然缺乏对染色质如何 结构甚至影响转录调控。染色质调节剂广泛涉及 人类癌症和其他疾病，是有吸引力的药物靶点，使染色质结构 并发挥作用是现代分子生物学和医学的关键目标。 我们对染色质功能的理解大多来自于相对静态的研究， 单一生长条件。在这项资助的头五年里，我的实验室已经扩展了典型的 从静态的基因组染色质分析到动态的背景，揭示了大量新的生物学 这只能在细胞不处于稳态条件下时才能理解。 在这里，我们计划集中在两个不同的时间尺度上的染色质动力学。第一 该项目关注转录变化过程中染色质结构的变化，以及 染色质在转录调控中的作用。对模式基因的经典研究表明，许多染色质 调节因子不影响稳态mRNA的产生，而是影响基因表达的速率。 对环境信号作出反应的诱导或抑制。通过进行基因组规模的 在数百个受到应激反应的染色质突变体中进行基因表达分析， 再加上全基因组映射的染色质结构转换下， 条件下，我们建议系统地剖析组蛋白修饰途径在酵母。 第二个项目涉及细胞周期中染色质结构的变化， 染色质作为表观遗传记忆的能力。我们之前对组蛋白的测量 跨多个细胞周期的动力学表明，组蛋白在细胞周期中扩散到约400 bp， 基因组复制这种测量对于染色质的保真度具有关键意义， 状态可能是遗传的，因为它将限制染色质结构域的潜在表观遗传 到那些~1 kb或更大。我们建议独立测量组蛋白的运动 蛋白质在基因组复制过程中，并分别表征组蛋白动力学上的 前导链和滞后链基因组。最后，我们将确定祖先的组蛋白 积累会影响基因调控。 总之，我们的研究提供了一个广泛的调查染色质结构， 在转录过程中和跨多个细胞周期的动态，并将提供一个改进的 理解染色质在基因调控和表观遗传中的功能的框架 传承

The packaging of eukaryotic genomes into chromatin affects DNA-templated processes from transcription to recombination, but we still lack a deep understanding of how chromatin structure even affects transcriptional regulation. Chromatin regulators are widely implicated in human cancers and other diseases and are attractive drug targets, making chromatin structure and function a key goal for modern molecular biology and medicine. Much of our understanding of chromatin function comes from relatively static studies in a single growth condition. Over the first five years of this grant, my laboratory has extended typical static genomic chromatin assays to dynamic contexts, revealing a great deal of novel biology that can only be appreciated when cells are not under steady-state conditions. Here, we plan to focus on chromatin dynamics at two different time scales. The first project concerns changes in chromatin structure during changes in transcription, and the role for chromatin in transcriptional control. Classic studies on model genes reveal that many chromatin regulators do not affect steady-state mRNA production, but rather affect the rate of gene induction or repression in response to environmental signals. By carrying out genome-scale gene expression analysis in hundreds of chromatin mutants subjected to a stress response, coupled with genome-wide mapping of chromatin structural transitions under the same conditions, we propose to systematically dissect histone modification pathways in yeast. The second project concerns changes in chromatin structure during the cell cycle and the capacity of chromatin to serve as epigenetic memory. Our prior measurements on histone dynamics across multiple cell cycles suggest that histones spread up to ~400 bp during genomic replication. This measurement has key implications for the fidelity with which chromatin states may be inherited, as it would limit potential epigenetic inheritance of chromatin domains to those ~1 kb or larger. We propose to independently measure the movement of histone proteins during genomic replication, and to separately characterize histone dynamics on the leading and lagging strand genomes. Finally, we will determine whether ancestral histone accumulation can affect gene regulation. Together, our studies provide a broad-based investigation into chromatin structural dynamics during transcription and across multiple cell cycles, and will provide an improved framework for understanding the function of chromatin in gene regulation and epigenetic inheritance.