Polyphosphate as a Novel Regulator of Super-Enhancer Complexes: Disruption of Phase Separation and Gene Expression

Inorganic polyphosphate (polyP) is a highly conserved linear polymer of orthophosphate, present across nearly all living organisms. Its functional diversity, particularly through recently discovered post-translational modifications, has garnered increasing scientific interest. However, its role in gene regulation, especially in mammalian systems, remains unexplored. In this study, we present findings that demonstrate that polyP multi-targets the super-enhancer complex to regulate gene expression, marking a novel mechanism of transcriptional control. We show that polyP modifies key components of the complex, including the Mediator subunit MED1, the coactivator Bromodomain-containing protein 4 (BRD4), and the transcriptional regulator Yin Yang 1 (YY1). This polyP-mediated modification not only disrupts their ability to undergo phase separation but also downregulates the expression of MED1 and BRD4, as well as impairs the nuclear localization of YY1. Furthermore, polyP inhibits YY1 dimer formation and disrupts YY1-mediated DNA looping, leading to suppressed gene expression. These discoveries highlight polyP as a novel regulator of super-enhancer-driven gene transcription and provide new insights into the broader role of polyP in epigenetic regulation. This work uncovers a previously unknown layer of gene control, positioning polyP as a critical player in transcriptional regulation through its interaction with transcription factors and coactivators. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/628164v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@10b53b2org.highwire.dtl.DTLVardef@a3dc10org.highwire.dtl.DTLVardef@1c4d72forg.highwire.dtl.DTLVardef@b7378_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPolyP modifies key components of the super-enhancer complex BRD4, MED1 and YY1 by targeting their His-rich, Lys-rich or PASK sequences C_LIO_LIPolyP disrupts phase separation of BRD4, MED1 and YY1 C_LIO_LIPolyP impairs YY1s recruitment of BRD4 and MED1 and disrupts nuclear localization, dimerization, DNA looping and DNA binding to YY1 C_LIO_LIPolyP attenuates gene expression mediated by YY1 and BRD4 C_LI