Transcriptional condensates at super-enhancers mediate pH-dependent transcriptional control in innate immunity

Tissue acidification is a common feature of hypoxia, inflammation and solid tumor. Acidic pH regulates innate immune response in macrophages by weakening BRD4-containing transcriptional condensates. Yet how disruption of transcriptional condensates leads to gene-specific regulation of immune programs remain unclear. Here, we integrated ATAC-seq, ChIP-seq, and RNA-seq of primary murine macrophages and performed integrative epigenomics analyses to identify transcriptional regulators (TRs) with pH-sensitive regulatory potential and association to BRD4-dependent transcriptional condensates. We determined pH-dependent super-enhancers (SEs) by extended profiles of BRD4 binding and h3K27ac marks. We found RELA, IRF family, and STAT family as candidate TRs enriched at BRD4-associated, pH-sensitive SE regions. RELA and IRF3 preferentially occupied BRD4-associated and pH-sensitive SEs, and displayed markedly reduced binding under acidic conditions, aligning with BRD4 occupancy change. Correspondingly, immune-response genes within BRD4-associated, pH-sensitive SE regions, including Ch25h, Acp2, Gda, and Ifit family, were significantly higher expressed at pH 7.4 than at pH 6.5. Together, these results reveal a set of TRs involved in BRD4-associated, pH-sensitive transcriptional condensates that coordinate macrophage gene activation under physiological conditions, providing mechanistic insight into how acidic stress modulates transcriptional condensates and immune responses.