Two distinct chromatin modules regulate proinflammatory gene expression [snMultiome]

Various mechanisms have been proposed to explain gene activation and co-regulation, including enhancer-promoter interactions via chromatin looping and the enrichment of transcription factors into hubs or condensates. However, these conclusions often stem from analyses of individual loci, and genome-wide studies exploring mechanistic differences in coupled gene expression are lacking. In this study, we dissected the proinflammatory gene expression program induced by TNFα in primary human endothelial cells using NGS- and imaging-based techniques. Our findings, enabled by our novel RWireX approach for single-cell ATAC-seq analysis, revealed two distinct regulatory chromatin modules: autonomous links of co-accessibility (ACs) between separated sites, and domains of contiguous co-accessibility (DCs) with increased local transcription factor binding. ACs and DCs associate with different transcriptional bursting kinetics, highlighting the existence of two structurally and functionally distinct regulatory chromatin modules in proinflammatory response. This identification provides a novel mechanistic framework for understanding how cells achieve both rapid and precise control of gene expression.