Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
STAR Protoc. 2022 Apr 12;3(2):101299. doi: 10.1016/j.xpro.2022.101299. eCollection 2022 Jun 17.
Here, we present a pipeline to map states of protein-binding DNA . Our pipeline infers as well as quantifies cooperative binding. Using dual-enzyme single-molecule footprinting (dSMF) data, we show how our workflow identifies binding states at an enhancer in S2 cells. Data from cells lacking endogenous DNA methylation are a prerequisite for this pipeline. For complete details on the use and execution of this protocol, please refer to Rao et al. (2021) and Krebs et al. (2017).
这里，我们提出了一个用于绘制蛋白质结合 DNA 状态的工作流程。我们的工作流程不仅可以推断出协同结合，还可以对其进行定量分析。通过双酶单分子足迹法（dSMF）数据，我们展示了如何使用我们的工作流程在 S2 细胞中的增强子上识别结合状态。该工作流程需要细胞中缺乏内源性 DNA 甲基化的数据。有关此方案的使用和执行的完整详细信息，请参考 Rao 等人（2021 年）和 Krebs 等人（2017 年）的研究。
