Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.

Regulation of the geroprotective histone-deacetylase SIRT1 is an important physiological strategy to protect against cardiovascular disease. SIRT1 activity regulates the oxidative stress response, DNA damage pathways, cell death, and cardioprotective SIRT1 levels decreases with age. Based on this and GWAS studies implicating misregulation linked to myocardial infarction risk, we hypothesized that disrupting proximal promoter regulation of SIRT1 causes cardiac stress. Focusing on Single Nucleotide Polymorphisms (SNPs) in the SIRT1 promoter, we used reporter gene assays to test if the transcriptional regulation of SIRT1 after oxidative stress is altered by the SNPs. Identifying a candidate A/G polymorphism at the -92 position in the promoter of SIRT1 , we show that the presence of the minority allele causes a disrupted epigenetic activation of SIRT1 . In model cell systems, binding of CCCTC-binding factor (CTCF) in the promoter of SIRT1 is reduced after oxidative stress in cells carrying the minority allele, correlating with a lack of activation of stress-protective SIRT1 expression in iPSC-derived cardiomyocytes. To investigate the physiological consequences of this mutation, we used Crispr/Cas9 to generate global Sirt1 promoter CTCF site mutant (Sirt1-mut) mice. Echocardiography in 7-month-old male mice shows reduced FS% (control 31.1±1.5%, Sirt1-mut 20.9±0.8%, mean±sem, p<0.0001, n=10-12 each), as well as increased LVIDs and decreased LVPWd wall dimensions in Sirt1-mut mice. RNA-seq on left ventricular cardiac tissue of 8-month-old control and Sirt1-mut mice identified 130 genes that are differentially regulated. Gene Ontology term enrichment analysis finds the differentially expressed genes are in pathways linked to regulation in response to reactive oxygen species and oxidative stress. In conclusion, we show that a mutation in the Sirt1 promoter critical for oxidative stress responses leads to systolic cardiac dysfunction. The transcriptional regulation of cardioprotective SIRT1 is an important and hitherto overlooked factor in the pathophysiology of heart failure.

Late-stage colorectal cancer (CRC) is still a clinically challenging problem. The activity of the tumor suppressor p53 is regulated via post-translational modifications (PTMs). While the relevance of p53 C-terminal acetylation for transcriptional regulation is well defined, it is unknown whether this PTM controls mitochondrially mediated apoptosis directly. We used wild-type p53 or p53-negative human CRC cells, cells with acetylation-defective p53, transformation assays, CRC organoids, and xenograft mouse models to assess how p53 acetylation determines cellular stress responses. The topoisomerase-1 inhibitor irinotecan induces acetylation of several lysine residues within p53. Inhibition of histone deacetylases (HDACs) with the class I HDAC inhibitor entinostat synergistically triggers mitochondrial damage and apoptosis in irinotecan-treated p53-positive CRC cells. This specifically relies on the C-terminal acetylation of p53 by CREB-binding protein/p300 and the presence of C-terminally acetylated p53 in complex with the proapoptotic BCL2 antagonist/killer protein. This control of C-terminal acetylation by HDACs can mechanistically explain why combinations of irinotecan and entinostat represent clinically tractable agents for the therapy of p53-proficient CRC.