Robust 4C-seq data analysis to screen for regulatory DNA interactions. Mus musculus

Regulatory DNA elements can control expression of distant genes via physical interactions. Here, we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using Chromosome Conformation Capture combined with high-throughput sequencing (4C-Seq) data. Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation.调控性DNA元件（Regulatory DNA elements）可通过物理相互作用调控远端基因的表达。本研究提出了一种经济高效的实验方案与计算分析流程，可基于染色体构象捕获结合高通量测序（Chromosome Conformation Capture combined with high-throughput sequencing，4C-Seq）数据，对选定的启动子及其他功能元件周边的染色质物理组织结构进行稳健表征。该方法可实现多重实验，并可常规与其他功能基因组学检测手段整合，从而助力基因调控的物理特征解析。