ArticleBMC genomics2014
Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
- Transgenerational inheritance of altered H3K27me3 in wild-type Caenorhabditis elegans.The EMBO journal · 2026Article
- Hypoxia-induced metastatic heterogeneity in pancreatic cancer.Nature communications · 2026Article
- Hypoxia-induced metastatic heterogeneity in pancreatic cancer.Research square · 2025Article
- Distinct regulatory mechanisms by the nuclear Argonautes HRDE-1 and NRDE-3 in the soma of Caenorhabditis elegans.G3 (Bethesda, Md.) · 2025Article
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- Two H3K23 histone methyltransferases, SET-32 and SET-21, function synergistically to promote nuclear RNAi-mediated transgenerational epigenetic inheritance inbioRxiv : the preprint server for biology · 2024Article
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- HRDE-2 drives small RNA specificity for the nuclear Argonaute protein HRDE-1.Nature communications · 2024Article
- Target-dependent suppression of siRNA production modulates the levels of endogenous siRNAs in the Caenorhabditis elegans germline.Development (Cambridge, England) · 2022Article
- Dual roles for nuclear RNAi Argonautes in Caenorhabditis elegans dosage compensation.Genetics · 2022Article
- Reprogramming the piRNA pathway for multiplexed and transgenerational gene silencing in C. elegans.Nature methods · 2022Article
- Coordinated maintenance of H3K36/K27 methylation by histone demethylases preserves germ cell identity and immortality.Cell reports · 2021Article
- Small RNAs and chromatin in the multigenerational epigenetic landscape ofPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Review
- Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression.BMC biology · 2020Article
- A Small-RNA-Mediated Feedback Loop Maintains Proper Levels of 22G-RNAs in C. elegans.Cell reports · 2020Article
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- RNAi pathways repress reprogramming of C. elegans germ cells during heat stress.Nucleic acids research · 2020Article
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- Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants.Nature cell biology · 2020Article
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3 authors.
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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.
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