Structural Annotation of the Human Genome

摘要 基因组的三维结构对基因调控至关重要 表达，维持基因组稳定性和染色体遗传。在过去的几年里 几年来，我们对空间的认识有了极大的增长 染色体的排列，这导致了对分子的洞察 调节基因的机制，以及基因组折叠缺陷如何导致人类 疾病。我们开发了强大的分子和基因组技术，基于 染色体构象捕捉(3C，5C，Hi-C)探测三维 染色体的结构。当细胞经历细胞分裂周期时，染色体 在两种完全不同的空间构象之间交替。我们和其他人已经使用了 基于3C的分析以确定人类基因组在间期和中期的结构 中期。在间期，基因组由几种不同类型的 染色体结构域，而在这些结构域中，基因受特定的 基因及其调控元件之间的循环相互作用。一种不同的结构是 在有丝分裂细胞中观察到，此时染色体变得高度紧凑。我们发现 在有丝分裂染色体中，它折叠成连续的染色质环的线性阵列。我们 描绘了一系列折叠中间体，显示了界面是如何 构象转换为中期状态。这些中间体包括 前期的扩展线性循环阵列和更紧凑的嵌套螺旋阵列 在前中期形成环状。这些研究带来了重要的新问题，我们的目标是 地址。首先，在基因组细节上还不知道在前期是如何进行间期的。 状态被擦除，染色体形成初始环阵列，姐妹染色单体成为 分居了。其次，人们对折叠的分子机器知之甚少 染色体。我们提出了创新的新战略，以确定 这些机器在有丝分裂和间期起作用。第三，我们假设这些 机器通过特定的顺式元素进行操作，这些顺式元素决定了它们如何以及在哪里获得 加载到染色体上，移动到新的位置，并在其他位置积累。我们会 识别和描述这些编码基因组折叠方式的DNA元件。我们的 拟议中的研究将揭示基因组如何折叠、展开和重新折叠。

Summary The three-dimensional organization of the genome is critical for regulation of gene expression, maintenance of genome stability and chromosome inheritance. Over the last several years there has been a tremendous increase in our knowledge of the spatial arrangements of chromosomes, and this is leading to insights into the molecular mechanisms that regulate genes, and how defects in genome folding can lead to human disease. We have developed powerful molecular and genomic technologies based on chromosome conformation capture (3C, 5C, Hi-C) to probe the three-dimensional structure of chromosomes. As cells go through the cell division cycle chromosomes alternate between two entirely different spatial conformations. We and others have used 3C-based assays to determine the structure of the human genome in interphase and in metaphase. In interphase the genome is composed of several different types of chromosomal domains, while within these domains genes are regulated by specific looping interactions between genes and their regulatory elements. A different structure is observed in mitotic cells, when chromosomes become highly compacted. We discovered that in mitosis chromosomes fold as linear arrays of consecutive chromatin loops. We have delineated a series of folding intermediates that show how the interphase conformation is converted into the metaphase state. These intermediates include extended linear loop arrays in prophase and more compacted helical arrays of nested loops in prometaphase. These studies lead to important new questions that we aim to address. First, it is not known in genomic detail how during prophase the interphase state is erased, chromosomes form initial loop arrays and sister chromatids become separated. Second, very little is known about the molecular machines that fold chromosomes. We propose innovative new strategies to identify new components of these machines that act during mitosis and interphase. Third, we hypothesize that these machines act through specific cis-elements that determine how and where they get loaded onto chromosomes, move to new sites and accumulate at yet other sites. We will identify and characterize these DNA elements that encode how the genome folds. Our proposed studies will uncover how the genome folds, unfolds and refolds.