In silico analysis and Predictive linkage of Deubiquitinating Enzymes underlying Early Development

Abstract Deubiquitinating enzymes (DUBs) exert their functions by catalyzing the ubiquitinated proteins and maintaining ubiquitination dynamics during post-translational modification. They carry out wide-gamut of functions in various cellular contexts by being associated with regulatory entities concerning transcription, translation, cell signalling, etc. However, limited studies are available concerning their specific attributes during organismal development. In this study, we have employed the integrated bioinformatics and experimental approaches to investigate the involvement of DUBs in embryonic stem cell (ESC) maintenance and differentiation. The StemMapper database revealed the distinctive expression profiles of various DUBs in ESCs and their differentiated derivatives. Further, experimental validation by qRT-PCR with a selected group of understudied DUBs including USP46, USP47, USP4, USP40, CYLD, and BRCC3 confirmed their expression patterns during cardiac and neural differentiation from ESCs, with USP46, USP47, and USP40 showing an increasing trend in contrast to USP4 during differentiation. While the TRANS-DSI database revealed novel DUB-Substrate interactions (DSI), the Gene Ontology and pathway enrichment analysis helped link these DUBs to critical cellular processes including transcriptional regulation, cell cycle control, and DNA repair. Further, the UbiBrowser 2.0 facilitated identifying several understudied DUBs as potential modulators of evolutionarily conserved developmental signalling cascades, notably Wnt, Notch, Hippo, and Hedgehog pathways. Our in silico analysis and predictions do provide crucial insights into the complex regulatory roles of DUBs in early development and establish a foundation for further investigations to unveil the molecular mechanisms and identify potential therapeutics thereof. Competing Interest Statement The authors have declared no competing interest.