Profiling Active Regulatory Elements in Archival Mouse Tissue by Formalin-Fixed Paraffin-Embedded Cleavage Under Targeted Accessible Chromatin

The standard for long-term storage of tissue samples is formalin fixation and paraffin embedding (FFPE), a method that allows samples to be archived at room temperature for decades. However, RNA degrades during storage, and prolonged exposure to ~4% formaldehyde damages RNA and DNA, limiting the utility of RNA sequencing for expression profiling. Our Cleavage Under Targeted Accessible Chromatin (CUTAC) adaptation of CUT&Tag for in situ open chromatin mapping provides high-resolution, genome-wide profiling of FFPE samples, including sections from decades-old tissue blocks. Here, we demonstrate a step-by-step on-slide FFPE-CUTAC protocol, using an antibody to RNA Polymerase II Serine-5 phosphate (RNAPII-S5p), which marks the transcriptional machinery at active regulatory elements when it is paused just before productive elongation, thereby capturing a proxy for active transcription. This workflow makes epigenomic profiling simple and affordable, opening the door to profiling archival samples for clinical applications, retrospective studies, basic transcriptome research, and broader translational research.