Chromatin-targeting small molecules cause class-specific transcriptional changes in pancreatic endocrine cells

Abstract

Under the instruction of cell-fate-determining, DNA-binding transcription factors, chromatin-modifying enzymes mediate and maintain cell states throughout development in multicellular organisms. Currently, small molecules modulating the activity of several classes of chromatin-modifying enzymes are available, including clinically approved histone deacetylase (HDAC) and DNA methyltransferase (DNMT) inhibitors. We describe the genome-wide expression changes induced by 29 compounds targeting HDACs, DNMTs, histone lysine methyltransferases (HKMTs), and protein arginine methyltransferases (PRMTs) in pancreatic α-and β-cell lines. HDAC inhibitors regulate several hundred transcripts irrespective of the cell type, with distinct clusters of dissimilar activity for hydroxamic acids and orthoamino anilides. In contrast, compounds targeting histone methyltransferases modulate the expression of restricted gene sets in distinct cell types. For example, we find that G9a/GLP methyltransferase inhibitors selectively up-regulate the cholesterol biosynthetic pathway in pancreatic but not liver cells. These data suggest that, despite their conservation across the entire genome and in different cell types, chromatin pathways can be targeted to modulate the expression of selected transcripts.histone modification | gene regulation | chemical epigenetics | beta cell biology | cholesterol pathway E pigenetic mechanisms mediated through chromatin control cell-state and cell-type decisions during development and in the adult (1, 2). Chromatin-modifying enzymes have been shown to function by interacting with master transcription factors, regulating the expression of key target genes and conferring epigenetic memory through the propagation of modifications to the chromatin template. These modifications include methylation of the DNA itself and a variety of posttranslational modifications to histones, the proteins most closely interacting with DNA. Depending on the type of modification, e.g., acetylation or methylation, and the exact position of the modified amino acid, these modifications can activate or repress transcription of the underlying DNA sequence (3).Small molecules targeting chromatin have mainly been developed for the treatment of cancer, justified by the identification of genetic aberrations leading to overexpression or activation of several chromatin-modifying enzymes (4-7). In contrast to clinically approved HDAC and DNMT inhibitors, fewer compounds targeting histone lysine methyltransferases (HKMTs) and protein arginine methyltransferases (PRMTs) are available. These small molecules are mainly used as chemical probe compounds in basic research, and toxicity is often limiting for testing in animal models. Interestingly, for most of the 50 HKMTs and 30 histone demethylases encoded in the human genome, no specific compounds are available. Even for HDACs, most compounds inhibit HDACs 1, 2, 3, and 6 (8), and HDAC8-specific compounds are only now emerging (9).Chromatin-modifying enzymes play important roles in normal development,...

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