Identification of DNA-Binding Factor Enrichment in Chromatin Accessibility Data to Define a Persister Cell Signature

Chemotherapy-resistant persister cells are a major driver of cancer recurrence, yet their epigenetic basis remains poorly characterized. This protocol describes a computational pipeline for identifying DNA-binding factors (DBFs) that are enriched in accessible chromatin that collectively define a persister cell signature (PCS). Starting from single-nucleus ATAC-seq (snATAC-seq) data processed through the 10x Genomics CellRanger ARC pipeline, this protocol covers (1) the creation of a Seurat/Signac object with ATAC peaks, (2) the optional integration of DNA-binding data from the ReMap2022 database as a per-cell chromatin module assay, (3) differential accessibility analysis across clinically defined comparison groups, and (4) identifying and defining the top enriched DBFs as the PCS. This approach is applicable to any snATAC-seq dataset in which cells can be grouped by clinical response, treatment status, or resistance phenotype. Key features • Integrated analysis of chromatin accessibility data with publicly available DNA-binding data is a useful technique to identify potential epigenetic biomarkers. • Single-nucleus ATAC-seq from clinically relevant samples can be used to identify binding enrichment of specific DNA-binding factors in sub-populations of cells. • This protocol was used to identify a persister cell signature that was able to predict chemotherapy resistance in high-grade serous ovarian cancer.