Project 1: Defining the Logic of Genome Organization In Pluripotent Cells

描述 这项提议的目标是揭示管理三维(3D)的机制 多能细胞中基因组的结构以及在重新编程到IPS细胞状态期间。染色体的空间组织是后生动物生物学中一个令人着迷的问题，但仍有许多悬而未决的问题，特别是破译驱动遗传基因座共定位的机制的挑战。 基于分化的细胞数据，细胞核中染色体相互作用的3D网络被认为是重要的，通过基因及其调节区的空间聚集和聚集在相同的亚核结构上的基因组，使得它们能够协调表达和调节表观遗传状态，从而维持细胞特性和影响基因表达。多能细胞基因组的3D结构基本上还没有被研究过。然而，最近我的实验室参与的一项关于DNA复制时间的研究表明，基因组的大规模重组与多能细胞致力于 分化，在种子层规范之前。这一过程的逆转似乎是重新编程的最后步骤之一，与重新编程因子与多能性基因靶标的结合以及全球染色质结构和DNA复制模式的变化有关。基于这些发现，我们假设，只有通过揭示多能细胞的空间组织之间的结构和功能关系，才能真正理解多能细胞和重编程过程中的基因组调控。 他指出，基因组和线性基因组特征，如染色质和表达状态，以及与转录因子的关系；建立多能核结构是重新编程的障碍。为了开始解决多能细胞中3D基因组的相互作用，我的实验室成功地建立了4C-SEQ方法来识别整个基因组中物理上接近Oct4基因座的区域，这表明该基因座与早期复制的、高表达的基因相互作用，这些基因被多能转录因子结合在一起，而这些基因本身在Oct4基因座上富含。基于这些广泛的工作，我们在重新编程和多能细胞染色质方面的专业知识，以及P01内部的具体合作和与P01生物信息学核心的紧密联系，我们处于有利地位，可以揭示管理人类和小鼠胚胎干细胞(ES)细胞3D基因组相互作用的分子机制，并研究在人类细胞重新编程期间分化的细胞基因组是如何重组的；以这些目标：

Description The goal of this proposal is to reveal the mechanisms that govern the three-dimensional (3D) architecture of the genome in pluripotent cells and during reprogramming to the IPS cell state. The spatial organization of chromosomes is a fascinating problem of metazoan biology, but leaves many unanswered questions, particularly the challenge to decipher the mechanisms driving the co-localization of genetic loci. Based on differentiated cell data, the 3D network of chromosomal interactions in the nucleus is thought to be important for the maintenance of cell identity and affect gene expression by spatial clustering of genes and their regulatory regions and by congregating groups of genes at the same sub-nuclear structure allowing their coordinated expression and modulation of epigenetic states. The 3D structure of the pluripotent cell genome is basically unstudied. However, a recent study of DNA replication timing, to which my lab contributed, suggested that a large-scale reorganization of the genome coincides with the commitment of pluripotent cells to differentiation, prior to germ layer specification. The reversal of this process appears to be one of the final steps of reprogramming, linked to the binding of the reprogramming factors to pluripotency gene targets and changes in global chromatin structure and DNA replication patterns. Based on these findings, we hypothesize that a true understanding of genome regulation in pluripotent cells and during reprogramming can only be obtained by revealing the structural and functional relationships between the spatial organization of the genome and linear genomic features such as chromatin and expression states and association with transcription factors; and that the establishment of the pluripotent nuclear architecture represents a road block to reprogramming. In an effort to begin to address 3D genomic interactions in pluripotent cells, my laboratory has successfully established the 4C-seq method to identify regions throughout the genome that are physically close to the Oct4 locus, which revealed that this locus interacts with early replicating, highly expressed genes that are bound by pluripotency transcription factors that themselves are enriched at the Oct4 locus. Based on this extensive work, our expertise in reprogramming and pluripotent cell chromatin, along with specific collaborations within the P01 and strong ties to the P01 Bioinformatics Core, we are well positioned to unveil molecular mechanisms governing the 3D genomic interactions in human and mouse embryonic stem (ES) cells and to study how the differentiated cell genome is reorganized during human cell reprogramming; with these Aims: