FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [mouse]

Fixed-Tissue ChIP-seq for H3K27Ac profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in FFPE tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27Ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and a minimized sonication step, to produce robust genome-wide H3K27Ac maps from clinical samples. We demonstrate FiTAc-seq suitability to generate high quality enhancer landscapes and SE annotation in a number of archived FFPE samples from distinct tumor types. This approach will be of great interest both for basic and clinical researchers. The entire protocol from FFPE blocks to sequence ready library can be accomplished within 4 days. FitAc-seq optimization on FFPE normal mouse liver tissue, testing different tissue homogenization temperatures and sonication times. Fit-seq protocol performance for H3K4me2 and H3K27Ac on FFPE normal mouse liver tissue. Matched fresh frozen mouse liver H3K27Ac ChIP-seq as control.