Orphan quality control shapes network dynamics and gene expression

All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-MYC oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over orphan transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression, while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers unique opportunities to modulate gene expression in disease. To investigate the global effect of UBR5 loss on gene expression, we generated a UBR5 knockout HEK 293T cell line using CRISPR. We then performed comparative gene expression profiling analysis via RNA-seq from both unedited (WT) and ∆UBR5 HEK 293T cells in biological triplicate. We also performed a similar anaylsis in H1 hESCs treated with either non-targeting control siRNAs or siRNAs against UBR5.