Spatially resolving chromatin landscapes in formalin-fixed paraffin-embedded tissues

Formalin-fixed paraffin-embedded (FFPE) samples represent an invaluable resource for histopathology research, but chromatin crosslinking in these fixed tissues precludes epigenomic analyses. Here, we present methods for reversing crosslinking in FFPE tissues followed by spatially resolved assay for transposase-accessible chromatin using sequencing (spatial-FFPE-ATAC) or cleavage under targets and tagmentation (spatial-FFPE-CUT&Tag). We applied spatial-FFPE-ATAC on adult mouse brain and revealed region-specific chromatin accessibility profiles with data quality comparable to standard ATAC-seq performed on fresh-frozen samples. Spatial-FFPE-ATAC delineated the epigenetic heterogeneity of clinical archival lymphoma of mucosa-associated lymphoid tissue and follicular lymphoma samples and uncovered tumor-specific karyotypes. Spatial-FFPE-ATAC traced cell proliferation by mitotic age inference and identified cholesterol-mediated cell proliferation in tumor cells. Spatial-FFPE-CUT&Tag in a transformed diffuse large B-cell lymphoma tissue revealed increased H3K27me3 occupancy at a chromosome 2 locus associated with tumor-specific copy number amplification. Therefore, spatial-FFPE-ATAC and spatial-FFPE-CUT&Tag enable genome-wide epigenomic profiling and epigenetic regulation investigations in archival FFPE samples. Overall design: Spatial-ATAC-seq or spatial-CUT&Tag on FFPE samples of mouse brain, mouse colon and human lymphoma.