droplet based high efficient chromatin conformation capture (DropHiChew)

Our research is focused on finding practical and cost-effective ways to extend our knowledge of the DNA dynamic movement. We've put to use the 10X single-cell systems to develop a user-friendly, droplet-based chromatin conformation capture technique called DropHiChew. This efficient process involves digesting single nuclei with enzymes, ligating nearby fragments, attaching adaptor sequences using Tn5, and packaging single cells with barcode gel beads via the 10X chromium system. After this, we carry out in-droplet reverse crosslinking and label each nucleus DNA with a barcode through linear amplification. Given that the 10X single cell system usually yields thousands of cells, a budget of 2M per cell could be beyond the budget for many labs. To capture the movement of DNA in depth, we've crafted a new algorithm, loop velocity, based on loop extrusion models. Our research indicates that even with shallow sequencing (50k contacts per cells), we can accurately gauge the speed and direction of cell development using our loop velocity algorithm. We're confident that this method has great potential for diverse applications in future chromatin capture studies.

本研究致力于探索实用且经济高效的手段，以深化我们对DNA动态运动的认知。我们借助10X单细胞系统（10X single-cell systems），开发出一款易用的基于液滴的染色质构象捕获技术——DropHiChew。该高效流程包含以下步骤：利用酶解单细胞核、连接邻近DNA片段、通过Tn5转座酶连接接头序列，以及借助10X Chromium系统将单细胞与带条形码的凝胶微珠进行包裹。随后，我们开展液滴内反向交联反应，并通过线性扩增为每个细胞核的DNA标记专属条形码。鉴于10X单细胞系统通常可获取数千个细胞，每个细胞2M的测序成本可能超出多数实验室的预算范围。为深入解析DNA运动机制，我们基于环挤出模型（loop extrusion models）开发了一款全新算法——环速度（loop velocity）。研究表明，即便采用低深度测序（每个细胞50k个接触位点），我们仍可通过该环速度算法精准研判细胞发育的速度与方向。我们相信该方法在未来的染色质捕获研究中具备广阔的多场景应用潜力。