NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

YAP is the key transcriptional effector of a highly conserved Hippo signaling pathway, from Drosophila (Yki) to humans (YAP). In our previous Drosophila screen, we identified NELFA, a core component of the promoter-proximal pausing (PPP) complex, as a suppressor of Yki-driven hyperproliferation.

Building on this observation, we investigated whether this PPP–YAP regulatory interaction is conserved in mammalian cells, using breast cancer as a model system. Using HEK293T and MDA-MB-231 cells, we demonstrate that NELFA depletion selectively amplifies YAP-driven transcription, thereby enhancing the expression of canonical YAP target genes. Whole-transcriptome analysis of NELFA-depleted MDA-MB-231 cells revealed widespread reprogramming upon NELFA loss, with strong enrichment of conserved YAP signatures, EMT and TGF-β pathways, and AP-1/TEAD-SMAD3 transcriptional networks—indicating that NELFA regulates a broad YAP-centered oncogenic module.