UBR5-mediated degradation of splicing and gene expression factors in normal and malignant states

Abstract

Nuclear processes constitute the foundation of cellular function, orchestrated by macromolecular assemblies such as the transcriptional and splicing machineries as well as epigenetic regulatory complexes. However, fluctuations in gene expression and translation caused by endogenous or exogenous sources, such as genotoxic and proteotoxic stress, threaten cellular homeostasis if not efficiently cleared. Therefore, nuclear protein quality control is essential for preserving genomic stability by facilitating the recognition and degradation of aberrant or misfolded proteins within the nucleus. UBR5 is an E3 ubiquitin ligase that has emerged as a systems-level regulator of nuclear protein homeostasis, coordinating orphan protein quality control. We systematically investigate the impact of UBR5 loss in malignant and non-malignant cellular contexts to identify conserved and context-specific UBR5-dependent quality control mechanisms. By integrating global proteomic and ubiquitylomic analyses, we demonstrate that UBR5 governs interconnected nuclear processes, including chromatin remodeling, transcriptional regulation, cell-cycle progression, and RNA metabolism. While UBR5 directly targets individual subunits, its predominant effect emerges at the level of multiprotein assemblies, where loss of UBR5 disrupts stoichiometric balance and induces coordinated protein-level shifts. We identify the intron-binding complex as the most prominent target of conserved UBR5 quality control regulation. Specifically, we show that AQR, a central scaffold subunit required for intron-binding complex formation, is a direct substrate of UBR5. Together with TRIP12, UBR5 governs AQR turnover and secures correct complex recycling. In summary, these findings advance our understanding of UBR5 as a central regulator of nuclear protein homeostasis in cancer and beyond, with direct involvement in quality control of the pre-mRNA splicing machinery through regulation of AQR.