Tessa M Firestone, Bryan J Venters, Katherine Novitzky, Liz Marie Albertorio-Sáez, Courtney A Barnes, Karlie N Fedder-Semmes, Nathan W Hall, Allison R Hickman, Mark Kaderli, Carolina Lin Windham, Matthew R Marunde, Danielle N Maryanski, Kelsey Noll, Leslie Lewis, Jennifer Spengler, Martis W Cowles, Zu-Wen Sun, Michael-Christopher Keogh, Andrea L Johnstone, Ellen N Weinzapfel, Lu Sun
The precise regulation of chromatin composition is critical to gene expression and cellular identity, and thus a key component in development and disease. Robust assays to study chromatin features, including histone post-translational modifications (PTMs) and chromatin-associated proteins (e.g., transcription factors or PTM readers), are crucial for understanding their function and identifying novel therapeutic strategies. To this end, Cleavage Under Targets and Release Using Nuclease (CUT&RUN) has emerged as a powerful tool for high-resolution epigenomic profiling. The approach has been successfully applied to numerous cell and tissue types, providing insights into target genomic distribution with unprecedented sensitivity and throughput. Here, we provide a detailed CUT&RUN protocol from sample collection through data analysis, including best practices and defined controls to ensure specific, efficient, and robust target profiling.