Tissular chromatin states cartography based on double-barcoded DNA arrays capturing unloaded PA-Tn5 Transposase

Recent developments in spatial omics are revoluzionating our understanding of tissue structures organization and their deregulation in disease. Here, we present a strategy for capturing chromatin histone modification signatures across tissue sections by taking advantage of a double-barcoded DNA arrays design compatible with in situ protein A-Transposase Tn5 tagmentation. This approach has been validated in presence of fresh-frozen mouse brain tissues but also in decalcified formalin-fixed paraffin-embedded (FFPE) mouse paws samples, where either the histone modification H3K4 tri-methylation or H3K27-acethylation has been used as proxy for interrogating active promoter signatures. Furthermore, since combinatorial enrichment of multiple histone modifications were shown to code for various states of gene transcriptional status (active, bivalent, repressed), we have integrated several histone modifications issued from consecutive mouse embryos to reveal changes in chromatin states across the tissue. Overall, this spatial epigenomics technology combined with the use of a spatial chromatin states analytical strategy paves the way for future epigenetics studies for addressing tissue architecture complexity. Tissue sections were deposited on DNA arrays presenting a MOS sequence at the 3'-end and two unique molecular barcodes associated to their physical position in the Array. After adding a 1st antibody directed to a given histone modification, and a second antibody for enhancing the signal, the ProteinA-Tn5 recombinant protein has been loaded into the DNA arrays thanks to the MOS sequence in regions enriched for the antibodies in use. Then, the use of MgCl2 allows to cleave the chromatin and allows to physically capture it into the DNA array. Finally a library preparation procedure is used for Illumina sequencing.