Panspecies Small-Molecule Disruptors of Heterochromatin-Mediated Transcriptional Gene Silencing

• Published in: Molecular and cellular biology 2015-02, Vol.35 (4), p.662-674
• Main Authors: Castonguay, Emilie, White, Sharon A., Kagansky, Alexander, St-Cyr, Daniel J., Castillo, Araceli G., Brugger, Christiane, White, Rachel, Bonilla, Carolina, Spitzer, Michaela, Earnshaw, William C., Schalch, Thomas, Ekwall, Karl, Tyers, Mike, Allshire, Robin C.
• Format: Article
• Language: English
• Subjects: Animals; Arabidopsis; Arabidopsis - drug effects; Arabidopsis - genetics; Arabidopsis - metabolism; Cell Cycle Proteins - antagonists & inhibitors; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; Cell Line, Tumor; Chromatin Assembly and Disassembly; Dioxanes - chemical synthesis; Dioxanes - chemistry; Dioxanes - pharmacology; DNA Methylation; Gene Expression Regulation, Fungal - drug effects; Gene Silencing - drug effects; Heterochromatin - chemistry; Heterochromatin - drug effects; Heterocyclic Compounds, 2-Ring - chemical synthesis; Heterocyclic Compounds, 2-Ring - chemistry; Heterocyclic Compounds, 2-Ring - pharmacology; Histone Methyltransferases; Histone-Lysine N-Methyltransferase - genetics; Histone-Lysine N-Methyltransferase - metabolism; Histones - genetics; Histones - metabolism; Mice; Piperazines - chemical synthesis; Piperazines - chemistry; Piperazines - pharmacology; Pyridines - chemical synthesis; Pyridines - chemistry; Pyridines - pharmacology; Schizosaccharomyces - drug effects; Schizosaccharomyces - genetics; Schizosaccharomyces - metabolism; Schizosaccharomyces pombe; Schizosaccharomyces pombe Proteins - antagonists & inhibitors; Schizosaccharomyces pombe Proteins - genetics; Schizosaccharomyces pombe Proteins - metabolism; Thiophenes - chemical synthesis; Thiophenes - chemistry; Thiophenes - pharmacology
• ISSN: 1098-5549; 0270-7306; 1098-5549
• DOI: 10.1128/MCB.01102-14

Heterochromatin underpins gene repression, genome integrity, and chromosome segregation. In the fission yeast Schizosaccharomyces pombe , conserved protein complexes effect heterochromatin formation via RNA interference-mediated recruitment of a histone H3 lysine 9 methyltransferase to cognate chromatin regions. To identify small molecules that inhibit heterochromatin formation, we performed an in vivo screen for loss of silencing of a dominant selectable kanMX reporter gene embedded within fission yeast centromeric heterochromatin. Two structurally unrelated compounds, HMS-I1 and HMS-I2, alleviated kanMX silencing and decreased repressive H3K9 methylation levels at the transgene. The decrease in methylation caused by HMS-I1 and HMS-I2 was observed at all loci regulated by histone methylation, including centromeric repeats, telomeric regions, and the mating-type locus, consistent with inhibition of the histone deacetylases (HDACs) Clr3 and/or Sir2. Chemical-genetic epistasis and expression profiles revealed that both compounds affect the activity of the Clr3-containing Snf2/HDAC repressor complex (SHREC). In vitro HDAC assays revealed that HMS-I1 and HMS-I2 inhibit Clr3 HDAC activity. HMS-I1 also alleviated transgene reporter silencing by heterochromatin in Arabidopsis and a mouse cell line, suggesting a conserved mechanism of action. HMS-I1 and HMS-I2 bear no resemblance to known inhibitors of chromatin-based activities and thus represent novel chemical probes for heterochromatin formation and function.