Journal Article

Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans

Peterman, Kimberly, Kalinava, Natallia, Chen, Esteban, Gu, Sam Guoping, Ni, Julie Zhouli

2017

Overview

Background Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to H3K9 trimethylation (H3K9me3) and transcriptional silencing at the target genes. H3K9me3 induced by either exogenous double-stranded RNA (dsRNA) or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in siRNA-mediated transcriptional silencing and inheritance of the silencing state at native target genes is unclear. In this study, we took combined genetic and whole-genome approaches to address this question. Results Here we demonstrate that siRNA-mediated H3K9me3 requires combined activities of three H3K9 histone methyltransferases: MET-2, SET-25, and SET-32. set - 32 single, met - 2 set - 25 double, and met - 2 set - 25;set - 32 triple mutant adult animals all exhibit prominent reductions in H3K9me3 throughout the genome, with met - 2 set - 25;set - 32 mutant worms losing all detectable H3K9me3 signals. Surprisingly, loss of high-magnitude H3K9me3 at the native nuclear RNAi targets has no effect on the transcriptional silencing state. 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. Conclusions Nuclear RNAi-mediated H3K9me3 in C. elegans requires multiple histone methyltransferases, including MET-2, SET-25, and SET-32. H3K9me3 is not essential for dsRNA-induced heritable RNAi or the maintenance of endo-siRNA-mediated transcriptional silencing in C. elegans . We propose that siRNA-mediated transcriptional silencing in C. elegans can be maintained by an H3K9me3-independent mechanism.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Animal Genetics and Genomics / Animals / Biomedical and Life Sciences / Caenorhabditis elegans / Caenorhabditis elegans - genetics / Caenorhabditis elegans - metabolism / Caenorhabditis elegans Proteins - antagonists & inhibitors / Caenorhabditis elegans Proteins - genetics / Caenorhabditis elegans Proteins - metabolism / Carrier Proteins - antagonists & inhibitors / Carrier Proteins - genetics / Carrier Proteins - metabolism / Cell Biology / Chromatin Immunoprecipitation / Gene Expression / Gene Function / Gene silencing / Genetic aspects / Genome / Genomic Instability / Germ Cells - metabolism / Health aspects / High-Throughput Nucleotide Sequencing / Histone-Lysine N-Methyltransferase - genetics / Histone-Lysine N-Methyltransferase - metabolism / Histones - genetics / Histones - metabolism / Human Genetics / Life Sciences / Methylation / Microscopy, Fluorescence / Mutagenesis / Plant Genetics and Genomics / Real-Time Polymerase Chain Reaction / RNA Interference / RNA, Double-Stranded - metabolism / RNA, Messenger - metabolism / RNA, Small Interfering - metabolism / Sequence Analysis, RNA / Transcription, Genetic / Virulence (Microbiology)