Determining the spatial organization of chromatin in cells mainly relies on crosslinking-based chromosome conformation capture techniques, but resolution and signal-to-noise ratio of these approaches is limited by interference from DNA-bound proteins. Here we introduce chemical-crosslinking assisted proximity capture (CAP-C), a method that uses multifunctional chemical crosslinkers with defined sizes to capture chromatin contacts. CAP-C generates chromatin contact maps at subkilobase (sub-kb) resolution with low background noise. We applied CAP-C to formaldehyde prefixed mouse embryonic stem cells (mESCs) and investigated loop domains (median size of 200 kb) and nonloop domains (median size of 9 kb). Transcription inhibition caused a greater loss of contacts in nonloop domains than loop domains. We uncovered conserved, transcription-state-dependent chromatin compartmentalization at high resolution that is shared from Drosophila to human, and a transcription-initiation-dependent nuclear subcompartment that brings multiple nonloop domains in close proximity. We also showed that CAP-C could be used to detect native chromatin conformation without formaldehyde prefixing.

确定细胞中染色质的空间组织主要依赖于基于交联的染色体构象捕获技术，但这些方法的分辨率和信噪比受到 DNA 结合蛋白的干扰的限制。在这里，我们介绍了化学交联辅助邻近捕获 (CAP-C)，这是一种使用具有定义尺寸的多功能化学交联剂来捕获染色质接触的方法。CAP-C 以亚千碱基 (sub-kb) 的分辨率生成低背景噪声的染色质接触图。我们将 CAP-C 应用于以甲醛为前缀的小鼠胚胎干细胞 (mESC) 并研究了环域（中位大小为 200 kb）和非环域（中位大小为 9 kb）。转录抑制导致非环域中的联系丢失比环域更大。我们发现了保守的，果蝇到人类，以及一个依赖转录起始的核子区室，使多个非环结构域紧密相连。我们还表明，CAP-C 可用于检测天然染色质构象而无需甲醛前缀。