Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans

Abstract

BackgroundSmall RNA-guided transcriptional silencing (nuclear RNAi) is fundamental to genome integrity and epigenetic inheritance. Despite recent progress in identifying the capability and genetic requirements for nuclear RNAi in Caenorhabditis elegans, the natural targets and cellular functions of nuclear RNAi remain elusive.MethodsTo resolve this gap, we coordinately examined the genome-wide profiles of transcription, histone H3 lysine 9 methylation (H3K9me) and endogenous siRNAs of a germline nuclear Argonaute (hrde-1/wago-9) mutant and identified regions on which transcription activity is markedly increased and/or H3K9me level is markedly decreased relative to wild type animals.ResultsOur data revealed a distinct set of native targets of germline nuclear RNAi, with the H3K9me response exhibiting both overlapping and non-overlapping distribution with the transcriptional silencing response. Interestingly LTR retrotransposons, but not DNA transposons, are highly enriched in the targets of germline nuclear RNAi. The genomic distribution of the native targets is highly constrained, with >99% of the identified targets present in five autosomes but not in the sex chromosome. By contrast, HRDE-1-associated small RNAs correspond to all chromosomes. In addition, we found that the piRNA pathway is not required for germline nuclear RNAi activity on native targets.ConclusionGermline nuclear RNAi in C. elegans is required to silence retrotransposons but not DNA transposon. Transcriptional silencing and H3K9me can occur independently of each other on the native targets of nuclear RNAi in C. elegans. Our results rule out a simple model in which nuclear Argonaute protein-associated-small RNAs are sufficient to trigger germline nuclear RNAi responses. In addition, the piRNA pathway and germline nuclear RNAi are specialized to target different types of foreign genetic elements for genome surveillance in C. elegans.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1157) contains supplementary material, which is available to authorized users.

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

“…To this end, we used published H3K9me3 ChIP-seq datasets in four different nrde mutants ( hrde-1, nrde-2, nrde-3 , and nrde-4 ; (Gu et al, 2012; Buckley et al, 2012; Ni et al, 2014). and analysed levels at genes and repeats upregulated in nrde-2 mutants or only in heterochromatin mutants.…”

The interplay between small RNA pathways shapes chromatin landscapes inC. elegans

“…Both histone marks can be artificially induced on active genes targeted by exogenous dsRNA (8,31,70), and several H3K9 methyltransferases have been connected to WAGO-induced silencing (30,(70)(71)(72). However, it was not possible to reliably correlate nuclear Argonautes' function in inhibiting endogenous genes with H3K9 methylation (34,35). Our results connect an increase in H3K9me3 to reduced transcription of CSR-1 target genes when CSR-1 is limited ( Figure 6A).…”

“…Both are capable of inducing H3K9me3 at genes complementary to exogenous dsRNA or at transgenes downstream of piRNAs (6,8,(28)(29)(30)(31)(32)(33). However, the interconnection between 22G-RNA production, H3K9 methylation and transcriptional silencing at the endogenous WAGO targets remains unclear (34,35).…”

MET-2, a SETDB1 family methyltransferase, coordinates embryo events through distinct histone H3 methylation states

“…RNAi pathways are critical to target heterochromatin machinery in worms and other organisms such as S. pombe (Moazed, 2009). In particular, the piwi pathway and the nuclear RNAi (nrde) pathway both target repeat sequences that make up the bulk of heterochromatin and are marked by H3K9me2 in C. elegans (Ashe et al, 2012;McMurchy et al, 2017;Ni et al, 2014;Weick and Miska, 2014). While it is known that the RNAi machinery targets H3K9 methylation, it was not clear whether these components dictate the timing of H3K9me2 in embryos.…”