Metazoan development hinges on pivotal signaling events that intricately regulate its diverse cellular processes. Posttranslational modifications (PTMs), such as ubiquitylation, play an important role by precisely modulating protein stability and turnover, ensuring protein homeostasis is maintained in a precise spatiotemporal manner throughout development. Ubiquitylation involves a meticulously orchestrated enzymatic cascade, beginning with an E1 ubiquitin activating enzyme, followed by a ubiquitin transfer to an E2 conjugating enzyme, and ending with an E3 ligase, which attaches ubiquitin to its target substrates. This cascade forms an elaborate and signaling code, forming monoubiquitin or polyubiquitin chains that govern diverse biological decisions based on cellular context and regulatory need of the modified substrate. Despite considerable advancements in discovering ubiquitin-dependent mechanisms in both health and disease, numerous questions remain unanswered. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex networks are established remains poorly understood. In Chapter 2, I describe the identification of a gene expression quality control pathway, where E3 ligase UBR5 degrades orphan transcriptional regulators which encompass a dynamic network of protein centered on oncoprotein c-Myc. Through cellular, biochemical, and structural experiments we show that UBR5 recognizes, binds, and degrades motifs that only unveil themselves upon complex dissociation. Rapid turnover of orphan subunits by UBR5 establishes dynamic interactions between transcriptional complexes to allow execution of gene expression. In Chapter 3, we begin exploring the relationship and pathway of UBR5 and master regulator of pluripotency, OCT4. I describe our preliminary understanding of how UBR5 recognizes OCT4 by generating a degron mutant and dimerization mutant of OCT4. Additional data which I will describe in this section shows that UBR5, OCT4, and c-MYC are part of a single gene expression circuit controlled by ubiquitylation. Further investigation is needed to fully uncover this quality control pathway important for preserving pluripotency. Finally, Chapter 4 unveils the discovery of a proteasome-dependent pathway involved in clearance of Huntingtin (HTT) oligomers. Using an imaging-based screen, we uncovered the key ubiquitin regulators of an oligomer clearance pathway. E3 ligase RNF126, its E2 UBE2K (also known as Huntingtin-interacting protein 2), and the VCP disaggregase are required for efficient proteasomal clearance of early HTT aggregates. These studies offer valuable insight into quality control networks crucial for preserving pluripotency, ensuring efficient execution of transcriptional programs, and facilitating clearance of Huntingtin oligomers. The discovery of these pathways paves the way for the development of target protein degradation strategies, leading to the creation of novel therapies aimed at improving patient outcomes.