Epigenomic Profiling of Histone Posttranslational Modifications in Frozen Cancer Tissue Using CUT&RUN

Alterations in the epigenetic landscape are now recognized as a hallmark of cancer. Among these, histone posttranslational modifications (HPTMs) represent a critical control layer, playing a significant role in chromatin remodeling and gene expression regulation. The comprehensive mapping of these modifications on a genome-wide scale is crucial for identifying regulatory regions and understanding downstream pathways, thereby providing a deeper and more integrated understanding of cancer biology. CUT&RUN (Cleavage Under Targets and Release Using Nuclease), combined with next-generation sequencing, is emerging as a highly reliable, low-background, and user-friendly technology for mapping antibody-bound chromatin regions in a genome-wide manner. In this chapter, we provide a comprehensive overview of an optimized protocol for targeting HPTMs in frozen tissue samples, emphasizing the crucial role of nucleus purification in our methodology.