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).
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9026571 | PMC |
| http://dx.doi.org/10.1016/j.xpro.2022.101299 | DOI Listing |
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