Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA.
Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, UCSF, San Francisco, California 94158, USA.
Nature. 2013 Dec 12;504(7479):306-310. doi: 10.1038/nature12716. Epub 2013 Nov 10.
In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space. However, the dynamic nature of chromatin connectivity has not been characterized at the genome-wide level. Here, through a chromatin interaction analysis with paired-end tagging approach using an antibody that primarily recognizes the pre-initiation complexes of RNA polymerase II, we explore the transcriptional interactomes of three mouse cells of progressive lineage commitment, including pluripotent embryonic stem cells, neural stem cells and neurosphere stem/progenitor cells. Our global chromatin connectivity maps reveal approximately 40,000 long-range interactions, suggest precise enhancer-promoter associations and delineate cell-type-specific chromatin structures. Analysis of the complex regulatory repertoire shows that there are extensive colocalizations among promoters and distal-acting enhancers. Most of the enhancers associate with promoters located beyond their nearest active genes, indicating that the linear juxtaposition is not the only guiding principle driving enhancer target selection. Although promoter-enhancer interactions exhibit high cell-type specificity, promoters involved in interactions are found to be generally common and mostly active among different cells. Chromatin connectivity networks reveal that the pivotal genes of reprogramming functions are transcribed within physical proximity to each other in embryonic stem cells, linking chromatin architecture to coordinated gene expression. Our study sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orchestrating development.
在多细胞生物中，转录调控是模拟谱系分化和细胞命运决定的核心机制之一。转录需要启动子与其相应的远端调控元件之间的动态染色质构型。人们认为，它们的通讯发生在三维核空间中聚合的 RNA 聚合酶形成的大离散焦点中，这些焦点被称为转录工厂。然而，染色质连接的动态性质尚未在全基因组水平上得到表征。在这里，我们通过使用主要识别 RNA 聚合酶 II 起始复合物的抗体进行的带有末端配对标签的染色质相互作用分析，探索了三种具有渐进谱系分化能力的小鼠细胞（包括多能胚胎干细胞、神经干细胞和神经球干细胞/祖细胞）的转录相互作用组。我们的全基因组染色质连接图谱揭示了大约 40000 个长程相互作用，提示精确的增强子-启动子关联，并描绘了细胞类型特异性的染色质结构。对复杂调控库的分析表明，启动子和远距离作用的增强子之间存在广泛的共定位。大多数增强子与位于其最近的活性基因之外的启动子相关联，这表明线性并列不是驱动增强子靶标选择的唯一指导原则。尽管启动子-增强子相互作用表现出高度的细胞类型特异性，但参与相互作用的启动子在不同细胞中通常是常见的并且大多是活跃的。染色质连接网络表明，重编程功能的关键基因在胚胎干细胞中彼此物理接近转录，将染色质结构与协调的基因表达联系起来。我们的研究为全面剖析空间和时间基因组结构及其在协调发育中的作用奠定了基础。
