High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [RNA-Seq]

Interactions between cis-regulatory elements such as promoters and enhancers are important for transcription but global identification of these interactions remains a major challenge. Leveraging the chromatin accessiblity of regulatory elements, we developed ARC-C (accessible region chromosome conformation capture), which profiles chromatin regulatory interactions genome-wide at high resolution. Applying ARC-C to C. elegans, we identify ~15,000 significant interactions at 500bp resolution. Regions bound by transcription factors and chromatin regulators such as cohesin and condensin II are enriched for interactions, and we use ARC-C to show that the BLMP-1 transcription factor mediates interactions between its targets. Investigating domain level architecture, we find that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) and that these domains interact to form A/B (active/inactive) compartment structure. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution. We performed RNA-seq replicates measuring polyA mRNA expression in wildtype and met2set25 C elegans L3 larvae.

启动子、增强子等顺式调控元件（cis-regulatory elements）之间的相互作用对转录过程至关重要，但在全基因组范围内鉴定这类相互作用仍是一项重大挑战。本研究借助调控元件的染色质可及性特性，开发了ARC-C（可及区域染色体构象捕获，accessible region chromosome conformation capture）技术，可在全基因组范围内以高分辨率解析染色质调控相互作用。将ARC-C技术应用于秀丽隐杆线虫（C. elegans），本研究在500bp分辨率下鉴定出约15000个显著相互作用。被转录因子及黏连蛋白（cohesin）、浓缩蛋白II（condensin II）等染色质调控因子结合的区域，其相互作用富集程度更高；本研究借助ARC-C技术证实，BLMP-1转录因子可介导其靶标之间的相互作用。在结构域层级的架构研究中，我们发现秀丽隐杆线虫中由活性或抑制性组蛋白修饰定义的染色质结构域可形成拓扑关联结构域（topologically associating domains, TADs），且这些结构域可进一步相互作用，形成A/B（活性/非活性）区室结构。ARC-C是一款可在高分辨率下解析基因组架构与调控相互作用的高效新型工具。本研究还开展了RNA测序（RNA-seq）重复实验，以检测野生型及met2set25秀丽隐杆线虫三龄（L3）幼虫的polyA信使RNA（polyA mRNA）表达水平。