Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

Formalin-fixed paraffin-embedded (FFPE) samples represent the gold standard for archiving pathology samples, and thus FFPE samples are a major resource of samples in clinical research. However, chromatin-based epigenetic assays in the clinical settings are limited to fresh or frozen samples, and are hampered by low chromatin yield in FFPE samples due to the lack of a reliable and efficient chromatin preparation method. Here, we introduce a new chromatin extraction method from FFPE tissues (Chrom-EX PE) for chromatin-based epigenetic assays.This study provided a new method that achieves efficient extraction of high-quality chromatin suitable for chromatin-based epigenetic assays with less damage on chromatin. During rehydration of FFPE tissues, applying a tissue-level cross-link reversal into the deparaffinized tissue at 65°C dramatically increased chromatin yield in the soluble fraction. The resulting chromatin is compatible with ChIP-seq for histone mark and chromatin-associated protein. The chromatin prepared by Chrom-EX PE showed a gradual fragmentation pattern with varying incubation temperature. At temperatures below 37°C, the majority of soluble chromatin is over 1 kb. The soluble chromatin prepared in the range of 45 - 60°C showed a typical nucleosomal pattern. And the majority of chromatin prepared at 65°C is close to mononucleosomal size.