The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
School of International Education, Beijing University of Chemical Technology, Beijing, 100029, China.
ACS Appl Mater Interfaces. 2024 Oct 2;16(39):52047-52058. doi: 10.1021/acsami.4c11280. Epub 2024 Sep 20.
Mapping genome-wide DNA-protein interactions (DPIs) provides insights into the epigenetic landscape of complex biological systems and elucidates the mechanisms of epigenetic regulation in biological progress. However, current technologies in DPI profiling still suffer from high cell demands, low detection sensitivity, and large reagent consumption. To address these problems, we developed DMF-ChIP-seq that builds on digital microfluidic (DMF) technology to profile genome-wide DPIs in a highly efficient, cost-effective, and user-friendly way. The entire workflow including cell pretreatment, antibody recognition, pA-Tn5 tagmentation, fragment enrichment, and PCR amplification is programmatically manipulated on a single chip. Leveraging closed submicroliter reaction volumes and a superhydrophobic interface, DMF-ChIP-seq presented higher sensitivity in peak enrichment than other current methods, with high accuracy (Pearson Correlation Coefficient (PCC) > 0.86) and high repeatability (PCC > 0.92). Furthermore, DMF-ChIP-seq was capable of processing the samples with as few as 8 cells while maintaining a high signal-to-noise ratio. By applying DMF-ChIP-seq, H3K27ac histone modification of early embryonic cells during differentiation was profiled for the investigation of epigenomic landscape dynamics. With the benefits of high efficiency and sensitivity in DPI analysis, the system provides great promise in studying epigenetic regulation during various biological processes.
绘制全基因组 DNA-蛋白质相互作用（DPIs）图谱提供了深入了解复杂生物系统表观遗传景观的途径，并阐明了生物进程中表观遗传调控的机制。然而，当前的 DPI 分析技术仍然存在细胞需求高、检测灵敏度低和试剂消耗大等问题。为了解决这些问题，我们开发了 DMF-ChIP-seq，它基于数字微流控（DMF）技术，以高效、经济且用户友好的方式对全基因组 DPIs 进行分析。整个工作流程包括细胞预处理、抗体识别、pA-Tn5 标签酶切、片段富集和 PCR 扩增，都在单个芯片上进行编程操作。利用封闭的亚微升反应体积和超疏水界面，DMF-ChIP-seq 在峰富集方面的灵敏度高于其他当前方法，具有高精度（Pearson 相关系数（PCC）>0.86）和高重复性（PCC>0.92）。此外，DMF-ChIP-seq 能够处理低至 8 个细胞的样本，同时保持高信噪比。通过应用 DMF-ChIP-seq，我们对分化过程中的早期胚胎细胞的 H3K27ac 组蛋白修饰进行了分析，以研究表观基因组景观动力学。该系统在 DPIs 分析中具有高效和高灵敏度的优势，为研究各种生物过程中的表观遗传调控提供了广阔的前景。
