Article: Disruption of Cardiac Med1 Inhibits RNA Polymerase-II Promoter Occupancy and Promotes Chromatin Remodeling

Authors: Duane D Hall, Kathryn M Spitler, and Chad E Grueter

Journal: Am J Physiol Heart Circ Physiol. 2018 Nov 21

Abstract:
The Mediator co-activator complex directs gene specific expression by binding distal enhancer-bound transcription factors through its Med1 subunit while bridging to RNA Polymerase-II (Pol-II) at gene promoters. In addition, Mediator scaffolds epigenetic modifying enzymes that determine local DNA accessibility. We previously found that deletion of Med1 in cardiomyocytes deregulates more than 5000 genes and promotes acute heart failure. We therefore hypothesize Med1 deficiency disrupts enhancer-promoter coupling. Using chromatin immunoprecipitation coupled deep sequencing (ChIP-seq, n=3 per ChIP assay) we find Pol-II pausing index is increased in Med1 knockout versus floxed control mouse hearts primarily due to a decrease in Pol-II occupancy at the majority of transcriptional start sites without a corresponding increase in elongating species. Parallel ChIP-seq assays reveal Med1-dependent gene expression correlates strongly with histone H3 K27 acetylation indicative of open and active chromatin at transcriptional start sites while H3 K27 tri-methylated levels, representing condensed and repressed DNA, are broadly increased and inversely correlate with absolute expression levels. Furthermore, Med1 deletion leads to dynamic changes in acetyl-K27 associated super-enhancer regions and their enriched transcription factor binding motifs that are consistent with altered gene expression. Our findings suggest that Med1 is important in establishing enhancer-promoter coupling in the heart and supports the proposed role of Mediator in establishing pre-initiation complex formation. We also find Med1 determines chromatin accessibility within genes and enhancer regions and propose the composition of transcription factors associated with super-enhancers changes in order to direct gene-specific expression.

Link to journal online: https://www.physiology.org/doi/abs/10.1152/ajpheart.00580.2018