Genomic analysis of histone replacement dynamics in yeast

描述（由申请人提供）：染色质在响应环境变化的不同时间尺度的过程中起着关键作用，需要快速的可塑性，而通过多代细胞的长期稳定性需要表观遗传的染色质。因此，了解活细胞中动态染色质状态的本质是非常有趣的。我们已经开发了能够在酵母基因组的很大一部分上以高分辨率快速测量染色质结构的工具，并且我们的实验室最近扩展了这些工具的使用，以测量g1阻滞酵母中整个酵母基因组的组蛋白H3替换动态。我们的初步数据使我们提出以下问题。在没有基因组复制的情况下，组蛋白替代的机制是什么？H3/H4和H2A/H2B的更替率有何不同？我们能机械地把这两个过程分开吗？组蛋白替代是否需要H3K56的乙酰化？它在G1骤停中的作用是什么？组蛋白替代在细胞周期中如何变化，异染色质沉默和染色体内聚等过程如何影响组蛋白替代？核小体替代是否使染色质结构域彼此隔离？大多数这些问题只能通过基因组分析来充分解决，因为在许多情况下，单位点研究可能会产生误导。我们已经开创了染色质结构的基因组分析的几种技术，并理想地定位于开展提出的研究。总的来说，提出的研究将提供一个非常有价值的窗口到染色质的动态性质。我们将确定组蛋白替代的机制，并将确定细胞周期在调节染色质压实状态稳定性中的作用。这些实验将极大地加深我们对染色质结构的基本认识，将扩大我们对转录控制的理解，并将限制染色质状态稳定遗传的任何模型。表观遗传，即DNA序列之外的信息遗传，是人体不同细胞类型之间差异的基础。在过去的十年里，人们越来越清楚地认识到，除了基因突变之外，表观遗传缺陷在癌症中也起着重要作用。在这个提议中，我们的目标是研究使细胞继承表观遗传信息的机制，希望我们最终可以利用这些信息来设计更直接的治疗癌症的方法。

DESCRIPTION (provided by applicant): Chromatin plays critical roles in processes governed in different time scales in response to environmental changes and requires rapid plasticity, while long term stability through multiple cell generations requires epigenetically heritable chromatin. It is of great interest, therefore, to understand the nature of dynamic chromatin states in living cells. We have developed tools that enable rapid measurement of chromatin structure at high resolution over a significant fraction of the yeast genome, and our lab has recently extended the use of these tools to measure histone H3 replacement dynamics across the entire yeast genome in G1-arrested yeast. Our preliminary data lead us to ask the following questions. What are the mechanisms for histone replacement in the absence of genomic replication? How do replacement rates differ for H3/H4 and H2A/H2B? Can we mechanistically separate those two processes? Is acetylation of H3K56 required for histone replacement, and what is its role during G1 arrest? How does histone replacement change during the cell cycle, and how do processes such as heterochromatin silencing and chromosome cohesion influence histone replacement? Does nucleosome replacement act to insulate chromatin domains from one another? Most of these questions can only be adequately addressed by genomic analysis, since in many cases single locus studies can be misleading. We have pioneered several techniques for genomic analysis of chromatin structure, and are ideally positioned to carry out the proposed studies. Taken together, the proposed studies will provide an immensely valuable window into the dynamic nature of chromatin. We will identify mechanisms of histone replacement, and will determine the role of cell cycle in regulation of the stability of chromatin compaction states. These experiments will greatly further our basic knowledge of chromatin structure, will expand our understanding of transcriptional control, and will constrain any models for the stable inheritance of chromatin states. Epigenetic inheritance, the inheritance of information beyond DNA sequence, underlies the differences between different cell types in the human body. In the past decade it has become increasingly clear that epigenetic defects, in addition to genetic mutations, play a major role in cancer. In this proposal we aim to investigate the mechanisms that enable cells to inherit epigenetic information, with the hope that we may eventually use this information to design more directed therapies against cancer.