Mediator Subunit MED16 Collaborates with UBP1-TFCP2 to Control Transcriptional Activation or Repression via Promoter Positional Specificity

The Mediator complex is an evolutionarily conserved transcriptional coactivator with well-characterized structure and function, though the roles of its dissociable subunits remain incompletely defined. Here, we demonstrate that Mediator subunit MED16 dissociates from the core complex to form a subcomplex with transcription factors UBP1 and TFCP2, and this interaction modulates transcriptional activation or repression in a context-dependent manner. Using protein purification coupled with mass spectrometry, we identified MED16 as a binding partner of UBP1-TFCP2. Gene expression analyses showed that UBP1 interacts with MED16 to activate a subset of silenced genes involved in lung homeostasis, angiogenesis, and cell proliferation. Conversely, the MED16-UBP1 interaction suppresses HIV-1 transcription, thereby reinforcing viral latency. Mechanistically, MED16 and UBP1 cooperatively bind the HIV-1 transcriptional start site (TSS) to inhibit preinitiation complex assembly. Genomic-scale analyses further demonstrated that transcription is activated when the UBP1-TFCP2 binding motif is proximal to the TSS, but repressed when the motif overlaps the TSS. Collectively, our findings identify a novel MED16-UBP1 interaction, define its dual role in transcriptional regulation, and highlight the therapeutic potential of targeting this axis in HIV-1 infection.