Panspecies small-molecule disruptors of heterochromatin-mediated transcriptional gene silencing

Emilie Castonguay, Sharon A. White, Alexander Kagansky, Daniel J. St-Cyr, Araceli G. Castillo, Christiane Brugger, Rachel White, Carolina Bonilla, Michaela Spitzer, William C. Earnshaw, Thomas Schalch, Karl Ekwall, Mike Tyers, Robin C. Allshire

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)662-674
Number of pages13
JournalMolecular and Cellular Biology
Volume35
Issue number4
DOIs
Publication statusPublished - 1 Jan 2015

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