一个全基因组尺度示踪染色质环重新生成的方法

染色质上非连续的两个DNA调控元件之间可由架构蛋白介导发生相互作用形成染色质环。各种类型的DNA调控元件（启动子、增强子、绝缘子等）之间形成的染色质环是细胞调控基因表达的重要方式之一，共同组成染色质的高级结构。人类细胞核内存在上万有序的染色质环结构。尽管它们的具体位置已经在很多细胞类型里得到了测定，关于驱动两个调控元件互相接触形成染色质环的机制却并不清楚。对染色质环形成过程的完整观测是研究这些机制的先决条件之一。我们将开发一种在细胞内示踪全基因组的染色质环重新生成的基因组学方法，可以追踪染色质环从萌发到稳态生成的全过程。此方法将偶联高通量测序技术，单组实验可实现对全基因组内绝大部分染色质环形成过程的完整观测。我们将系统测定染色质环形成过程的一些物理参数，譬如方向性与速度，并与其它染色质活动进行整合分析。本研究的预期结果将为染色质环的生成以及它们如何调控基因表达提供崭新的理论依据。

Two discontinuous DNA regulatory elements in mammalian genome can form a chromatin loop when brought together by architectural proteins. Chromatin loops formed between various types of elements, such as promoters, enhancers and insulators, are one of the most important ways to regulate gene expression, and collectively constitute the high order chromatin structure. There are tens of thousands of different chromatin loops in nucleus of mammalian cells. Although their precise location has been mapped by genomic methods in various cell types, the mechanisms driving the two regulatory elements to come together have been elusive. Tracking the complete process of chromatin loop formation is one of the prerequisites for demystifying these mechanisms. This study aims to develop a genome-wide method for tracking the de novo formation of chromatin loops, from their initiation to stabilization, on newly replicated chromatin. When coupled with high-throughput sequencing technology, formation of most of the chromatin loops in a genome can be potentially tracked and recorded in a single set of experiments. The biophysical features of the loop formation process, such as directionality and velocity, will be systematically measured and analyzed with other chromatin activities in an integrative way. The results from this study have great potential to uncover mechanisms underlying formation of chromatin loops and how they regulate gene expression.