Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (microarray)

Embryonic stem cells (ESCs) and induced-pluripotent stem cells (iPSCs) self-renew and differentiate into an array of cell types in vitro and in vivo. A complex network of genetic and epigenetic pathways regulates the self-renewal and differentiation of these pluripotent cells, and the structure and covalent modifications of chromatin play a prominent role in this process. We examine nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach that enabled the identification of regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. The majority of changes in nucleosomal signatures that occur in differentiation are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of pluripotency and likely identify key regulatory regions that play a role in determining cell identity. A six chip study using total RNA recovered from three cell types with 2 replicates each

胚胎干细胞（Embryonic Stem Cells，ESCs）与诱导多能干细胞（Induced-Pluripotent Stem Cells，iPSCs）可在体外及体内完成自我更新，并分化为多种细胞类型。由遗传与表观遗传通路构成的复杂网络，可调控这类多能细胞的自我更新与分化过程；染色质的结构与共价修饰在此过程中发挥关键作用。
本研究采用微球菌核酸酶测序（MNase-seq）技术，检测小鼠和人类的胚胎干细胞（ESCs）、诱导多能干细胞（iPSCs）以及分化细胞的核小体占据情况。为解决该技术固有的实验变异问题，我们开发了一种生物信息学方法，能够鉴定多能细胞与体细胞之间核小体占据存在差异的区域（Regions of Difference，RoD）。
分化过程中出现的多数核小体特征变化，会在重编程阶段被重置。我们据此得出结论：核小体占据情况的变化是多能性的标志性特征，且可用于识别参与细胞身份决定过程的关键调控区域。
本研究包含一项六芯片实验：从三种细胞类型中提取总RNA，每种细胞设置2次生物学重复。