The Nrde Pathway Mediates Small-RNA-Directed Histone H3 Lysine 27 Trimethylation in Caenorhabditis elegans

Abstract

Small-RNA-mediated chromatin modifications have been widely studied in plants and S. pombe. However, direct evidence of small-RNA-guided sequence-specific chromatin alterations is scarce in animals. In C. elegans, the nuclear RNAi defective (Nrde) pathway functions to transport siRNA from the cytoplasm to the nucleus, modulate transcription elongation, induce histone H3 lysine 9 (H3K9) trimethylation, and mediate transgenerational inheritance of RNAi. Here, we show that both exogenous RNAi and NRDE-bound endogenous 22G RNAs can direct sequence-specific histone H3 lysine 27 (H3K27) trimethylation at targeted loci through the Nrde pathway. The resulting H3K27me3 status can be inherited by progeny for multiple generations. piRNAs and WAGO-1-associated siRNAs induce H3K27 methylation as well. Interestingly, CSR-1-associated endogenous siRNAs fail to trigger H3K27 methylation, whereas exogenous provision of dsRNAs can induce H3K27 methylation at the CSR-1-targeted loci via the Nrde pathway. We further observed distinct genetic requirements of H3K9 and H3K27 trimethylation. Whereas set-25 and met-2 are required for K9 methylation, mes-2 is required for K27 methylation. The depletion of mes-2 leads to a nuclear RNAi defective phenotype. These results indicate that dsRNA-triggered chromatin modification is a sequence-specific response that engages the Nrde pathway in C. elegans.

A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress

“…Cytoplasmic silencing mechanisms are not well understood, but recent advances have been made in the understanding of transcriptional silencing. In the nucleus, the piRNA pathway engages a second small RNA pathway called the nuclear RNAi pathway (or nrde pathway), which orchestrates H3K9 and H3K27 methylation and/or inhibition of RNA Pol II (Guang et al, 2010; Burkhart et al, 2011; Mao et al, 2015; Alló and Kornblihtt, 2010). Although the nrde pathway can be triggered by the piRNA pathway in the germ line, it is also active in the soma, with dedicated Argonaute proteins for germ line (HRDE-1) and soma (NRDE-3) (Guang et al, 2010; Burkhart et al, 2011; Buckley et al, 2012; Guang et al, 2008).…”

Early Developmental Exposure to dsRNA Is Critical for Initiating Efficient Nuclear RNAi in C. elegans

“…Nuclear RNAi promotes histone H3K9 and histone H3K27 trimethylation, resulting in transcriptional silencing (Burton et al, 2011, Mao et al, 2015). One possibility is that cell division or development is coupled to nuclear RNAi.…”

MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality

“…Loss of the germline nuclear RNAi pathway by mutation of hrde-1 or nrde-1, -2 , or -4 leads to defective inheritance of silencing by nuclear RNAi, germline mortality, and a progressive depletion of H3K9me3 marks at endogenous target sites (Buckley et al, 2012). Although previous studies have implicated the histone methyltransferases SET-25 and MET-2 in siRNA-directed H3K9 methylation (Ashe et al, 2012; Mao et al, 2015), the mechanisms by which siRNAs regulate heterochromatin deposition and maintenance remain unclear.…”