RNA expression profiling for Paf1 complex mutant strains [miRNA]

Small RNA molecules are well known for silencing gene expression post-transcriptionally, but they are also implicated in epigenetic regulation across kingdoms. However, the mechanisms of epigenetic gene silencing by small RNAs are mostly unknown. In addition, stably silencing genes de novo using synthetic small RNAs to trigger locus-independent heterochromatin formation is impossible. Using fission yeast, we show that RNA-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 (Paf1) complex. Temporary expression of a synthetic hairpin RNA in Paf1 mutants triggers stable heterochromatin formation at homologous loci, effectively silencing genes in trans. This repressed state is propagated over many generations by continual production of secondary siRNAs, independently of the synthetic hairpin RNA. Our work uncovers a novel mechanism for small RNA-mediated epigenome regulation and highlights fundamental roles for the Paf1 complex and the RNA interference machinery in building epigenetic memory. Small RNA was extracted from wild-type and mutant strains to compare miRNA gene expression.