Bromodomain Containing Protein 4 (BRD4) Regulates Expression of its Interacting Coactivators in the Innate Response to Respiratory Syncytial Virus

Abstract

Bromodomain-containing protein 4 plays a central role in coordinating the complex epigenetic component of the innate immune response. Previous studies implicated BRD4 as a component of a chromatin-modifying complex that is dynamically recruited to a network of protective cytokines by binding activated transcription factors, polymerases, and histones to trigger their rapid expression via transcriptional elongation. Our previous study extended our understanding of the airway epithelial BRD4 interactome by identifying over 100 functionally important coactivators and transcription factors, whose association is induced by respiratory syncytial virus (RSV) infection. RSV is an etiological agent of recurrent respiratory tract infections associated with exacerbations of chronic obstructive pulmonary disease. Using a highly selective small-molecule BRD4 inhibitor (ZL0454) developed by us, we extend these findings to identify the gene regulatory network dependent on BRD4 bromodomain (BD) interactions. Human small airway epithelial cells were infected in the absence or presence of ZL0454, and gene expression profiling was performed. A highly reproducible dataset was obtained which indicated that BRD4 mediates both activation and repression of RSV-inducible gene regulatory networks controlling cytokine expression, interferon (IFN) production, and extracellular matrix remodeling. Index genes of functionally significant clusters were validated independently. We discover that BRD4 regulates the expression of its own gene during the innate immune response. Interestingly, BRD4 activates the expression of NFκB/RelA, a coactivator that binds to BRD4 in a BD-dependent manner. We extend this finding to show that BRD4 also regulates other components of its functional interactome, including the Mediator (Med) coactivator complex and the SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin (SMARC) subunits. To provide further insight into mechanisms for BRD4 in RSV expression, we mapped 7,845 RSV-inducible Tn5 transposase peaks onto the BRD4-dependent gene bodies. These were located in promoters and introns of cytostructural and extracellular matrix (ECM) formation genes. These data indicate that BRD4 mediates the dynamic response of airway epithelial cells to RNA infection by modulating the expression of its coactivators, controlling the expression of host defense mechanisms and remodeling genes through changes in promoter accessibility.

Bromodomains in Human-Immunodeficiency Virus-Associated Neurocognitive Disorders: A Model of Ferroptosis-Induced Neurodegeneration

“…In addition, BRD4 promotes iron sequestration in ferritin to withhold it from pathogens, likely implicating this protein in nutritional immunity ( Sui et al, 2019 ). Moreover, BRD4 displays direct antiviral properties, including inhibition of HIV Tat antigen, hence viruses must neutralize this protein to thrive ( Wang et al, 2020 ; Alamer et al, 2021 ; Xu X. et al, 2021 ; Table 1 ). Indeed, several viruses, including HIV and SARS-CoV-2 have developed the ability to usurp BRD4, overcoming nutritional immunity ( Chen I. P. et al, 2021 ).…”

Selective Inhibition of Bromodomain-Containing Protein 4 Reduces Myofibroblast Transdifferentiation and Pulmonary Fibrosis

“…The mechanisms behind how selective BRD4 BD inhibitors disrupt epigenetic control are just beginning to be understood. We recently found that inhibition of BRD4 BDs disrupt association of more than 200 transcription factors in the activated complex ( Mann et al, 2021 ), and that BRD4 inhibitors block expression of key components of transcriptional coactivators, chromatin remodeling proteins as well as BRD4 itself ( Xu et al, 2021 ). Consequently, follow-up studies are needed to determine the mechanisms by which ZL0591 disrupts and reverses bleomycin-induced fibrosis in mice.…”

The Hexosamine Biosynthetic Pathway Links Innate Inflammation With Epithelial-Mesenchymal Plasticity in Airway Remodeling

“…In addition, BRD4 controls expression of members of its interacting coactivators that bind the BD, including transcription factors, adaptors and chromatin remodeling complexes. Reproduced with permission from ( Xu et al, 2021a ).…”

“…To address the question whether BRD4 dependent genes are regulated by changes in chromatin accessibility, we mapped the BRD4-dependent gene regulatory network to 1700 chromatin-accessible sites in the genome determined by Tn5 transposase-cleavage-next generation sequencing (ATAC-Seq) studies ( Xu et al, 2020 ). Genome ontology and pathway enrichment indicated a substantial enrichment of genes controlling ECM biosynthesis and/or modification ( Xu et al, 2021a ). Specifically, we found that RSV produces nucleosome-free regions on TGFB1/JUNB//FN1/MMP9 genes and GFPT2 ( Xu et al, 2020 ) ( Figure 7 ).…”