E3 ubiquitin ligases of the tripartite motif (TRIM) family have emerged as critical regulators of transcription factor activity, integrating genomic recognition with chromatin and ubiquitin signalling. While TRIM paralogues such as Trim24, Trim28, and Trim33 share conserved domain structures that support homo‑ and heterodimerization, how functional specificity is achieved remains unclear. We previously identified Trim24 as a repressive cofactor for p53, using its PHD–bromodomain to interpret epigenetic marks that restrict its activity on the genome.
Here, we extend this approach to systematically map genome‑wide recruitment of Trim24, Trim28, and Trim33 across multiple genomic contexts. Our data reveal that genomic recruitment is governed primarily by transcription factor selectivity, with distinct TRIM– transcription factor partnerships showing minimal redundancy even at shared chromatin states. Motif analysis and perturbation in stem cells support a model in which these paralogues have diversified by evolving unique transcription factor interaction surfaces while maintaining common chromatin‑binding modules. This provides a mechanistic framework for how this family of ubiquitin ligases achieve functional specificity, and suggests that targeting individual TRIM–transcription factor axes could offer precision strategies for modulating ubiquitin‑dependent genomic regulation in disease contexts.