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

Introduction

Bromodomain-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.

Methods

To 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.

Results

We 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.

Discussion

These 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.

Supramolecular Reinforcement of a Large-Pore 2D Covalent Organic Framework

Two-dimensional covalent organic frameworks (2D-COFs) are a class of crystalline porous organic polymers that consist of covalently linked, two-dimensional sheets that can stack together through noncovalent interactions. Here we report the synthesis of a novel COF, called PyCOFamide, which has an experimentally observed pore size that is greater than 6 nm in diameter. This is among the largest pore size reported to date for a 2D-COF. PyCOFamide exhibits permanent porosity and high crystallinity as evidenced by the nitrogen adsorption, powder X-ray diffraction, and high-resolution transmission electron microscopy. We show that the pore size of PyCOFamide is large enough to accommodate fluorescent proteins such as Superfolder green fluorescent protein and mNeonGreen. This work demonstrates the utility of noncovalent structural reinforcement in 2D-COFs to produce larger and persistent pore sizes than previously possible.