Interleukin-18 induced chromatin accessibility coupled to proteomic analysis by mass cytometry and ion beam imaging

Regulated chromatin states control genome accessibility and thus influence gene expression. Here we report an analysis pipeline termed ATAC-mass that capitalizes on isotopic labeling to detect the accessible genome by multiplexed ion beam imaging (MIBI) and mass cytometry. With MIBI the accessible genome can be visualized at approximately 100-nm resolution simultaneously with metabolic labeling to enable multi-parameter three-dimensional imaging of nuclear features. Extension of this approach to non-spatial mass cytometry enabled the simultaneous measurement of multiple parameters and total genome accessibility in millions of individual cells. We used ATAC-mass to analyze natural killer cells after stimulation with interleukin (IL)-12 or IL-18 -- demonstrating that IL-18 treatment leads to increased total genome accessibility. Analysis of the spatial organization of open chromatin suggest that IL-12 and IL-18 both induce an increase in chromatin accessibility in noncompacted DNA regions. Deep sequencing of the genomic distribution of open chromatin revealed that IL-18 increased the accessibility of quiescent enhancers whereas genomic loci that become more accessible by IL-12 stimulation are mainly localized in the active promoter regions. This integration of epigenomics, proteomics and high-resolution imaging at the single-cell level provides a tool that can enhance our appreciation of the molecular mechanisms underlying gene regulation. ATAC-seq with MIBI compatible Tn5 and IL12/IL18 treated NKL cells Each *bw file was generated from both rep1, rep2 and is linked to the corresponding rep1 sample records. All the Cluster*.bed files were generated from the NK*.fastq.gz and NK*.bw files. Please note that the ATAC-mass Tn5 samples were used for assay validation, with no unique processed files aside from basic alignment as described in the associated publication. It shows that the methodology works in comparison to the original ATAC paper [PMID 24097267].