The role of heterochromatin in RNAi-mediated transcription repression in C. elegans

The germline nuclear RNAi pathway in C. elegans can lead to histone H3 lysine 9 trimethylation (H3K9me3) and transcriptional silencing at target genes. H3K9me3 heterochromatin induced by either exogenous double-stranded RNA (dsRNA) or endogenous siRNA (endo-siRNA) is highly specific to the target loci and is trans-generationally heritable. Despite these features, the role of H3K9me3 in siRNA-mediated establishment and maintenance of transcriptional silencing and its inheritance in C. elegans is unclear. It is also not known which of H3K9me3 histone methyltransferases (HMT) function in an RNAi-dependent manner. In this study, we took combined genetic, biochemical, CRISPR-Cas9 genome editing, cell biology and computational approaches to address these questions. Here we demonstrate that siRNA-mediated H3K9me3 requires combined activities of three H3K9 histone methyltransferases (HMTs): MET-2, SET-25, and SET-32. Surprisingly, loss of high-magnitude of H3K9me3 in set-32; met-2 set-25 mutant worms has no effect on the transcriptional silencing at the native nuclear RNAi targets. In addition, the exogenous dsRNA-induced transcriptional silencing and heritable RNAi at oma-1, a well-established nuclear RNAi reporter gene, are completely resistant to the loss of H3K9me3. Repair of germline nuclear Argonaut HRDE-1 fully restore silencing of nuclear RNAi targets. However, loss of SET-32 showed trans-generational delay in re-establishment of transcriptional silencing. We propose that H3K9me3 is dispensable for the maintenance of siRNA-mediated transcriptional silencing. However, H3K9me HMT SET-32 promotes the onset of nuclear RNAi-mediated transcriptional silencing. Ph.D.Includes bibliographical referencesby Natallia Kalinav