Wang Jingjing, Meng Xianwen, Chen Hongjun, Yuan Chunhui, Li Xue, Zhou Yincong, Chen Ming
Brief Funct Genomics. 2016 Sep;15(5):385-95. doi: 10.1093/bfgp/elv062. Epub 2016 Jan 14.
Developments in chromosome conformation capture (3C) technologies have revealed that the three-dimensional organization of a genome leads widely separated functional elements to reside in close proximity. However, the mechanisms responsible for mediating long-range interactions are still not completely known. In this review, we firstly evaluate and compare the current seven 3C-based methods, summarize their advantages and discuss their limitations to our current understanding of genome structure. Then, software packages available to perform the analysis of 3C-based data are described. Moreover, we review the insights into the two main mechanisms of long-range interactions, which regulate gene expression by bringing together promoters and distal regulatory elements and by creating structural domains that contain functionally related genes with similar expression landscape. At last, we summarize what is known about the mediating factors involved in stimulation/repression of long-range interactions, such as transcription factors and noncoding RNAs.
染色体构象捕获（3C）技术的发展表明，基因组的三维组织使得广泛分离的功能元件紧密相邻。然而，介导长程相互作用的机制仍不完全清楚。在本综述中，我们首先评估和比较当前七种基于3C的方法，总结它们的优点并讨论其局限性，以便我们目前对基因组结构的理解。然后，描述了可用于分析基于3C数据的软件包。此外，我们回顾了对长程相互作用的两种主要机制的见解，这两种机制通过将启动子和远端调控元件聚集在一起以及通过创建包含具有相似表达格局的功能相关基因的结构域来调节基因表达。最后，我们总结了关于参与刺激/抑制长程相互作用的介导因子的已知信息，例如转录因子和非编码RNA。
