Bromodomain-containing Protein 4 regulates innate inflammation via modulation of alternative splicing

Abstract

IntroductionBromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In the context of airway viral infection, BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream epithelial plasticity. Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not well understood. Given BRD4's interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing.MethodsTo address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i.ResultsWe discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 (IFRD1) and X-Box Binding Protein 1 (XBP1), related to the innate immune response and the unfolded protein response (UPR). We identify requirement of BRD4 for expression of serine-arginine splicing factors, splicosome components and the Inositol-Requiring Enzyme 1 IREα affecting immediate early innate response and the UPR.DiscussionThese findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing via modulating splicing factor expression in virus-induced innate signaling.

Cooperative interaction of interferon regulatory factor -1 and bromodomain—containing protein 4 on RNA polymerase activation for intrinsic innate immunity

“…We next explored the nature of interaction between IRF1 and BRD4 in the intrinsic innate response. BRD4 contains two highly conserved N-terminal bromodomains (BDs), BD1 and BD2, which mediate RSV-inducible interactions with ~100 proteins including transcription factors, chromatin regulators, spliceosome components, mediator proteins and polymerases ( 63 – 65 ); note in this analysis, IRF1 was not observed in the BRD4 CRC). We hypothesized that BRD4 BD serves to recruit coactivator complexes that function independently of its interaction with the PTEF-b complexes; complexes that interact with the COOH terminal BET domain ( 66 ).…”

“…RSV infection increases ~100 proteins to bind the BRD4 complex ( 64 , 77 ). Through these associated proteins, BRD4 plays multiple functional roles in the coordinate genome innate response, including transcriptional elongation, stimulating enhancer remodeling, and mediating alternative mRNA splicing ( 65 ).…”

“…In a distinct mechanism, we have recently demonstrated that BRD4’s interaction with spliceosome promotes alternative mRNA splicing of a subset of IIR genes ( 65 ). One of these pathways controlled by BRD4 alternative splicing is the unfolded protein response, a critical pathway in the intrinsic IIR and metabolic adaptations to RSV infection ( 34 , 76 ).…”

BRD4 as a Therapeutic Target in Pulmonary Diseases

“…BRD4 interactome analysis has uncovered approximately 100 proteins that are enriched in the BRD4 complex and responsive to respiratory syncytial virus (RSV)-infection and BRD4 inhibition [11], which is related to the BRD4's acetyl-lysine binding bromodomains. In addition, several studies also reported the role of BRD4 in regulating alternative splicing to control cell differentiation, heat shock response, and innate immune response [12][13][14].…”