Gu SG, Pak J, Guang S, Maniar JM, Kennedy S, Fire A. Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint. Nat Genet 44: 157-164

Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.
Nature Genetics (Impact Factor: 29.35). 02/2012; 44(2):157-64. DOI: 10.1038/ng.1039
Source: PubMed


Exogenous double-stranded RNA (dsRNA) has been shown to exert homology-dependent effects at the level of both target mRNA stability and chromatin structure. Using C. elegans undergoing RNAi as an animal model, we have investigated the generality, scope and longevity of dsRNA-targeted chromatin effects and their dependence on components of the RNAi machinery. Using high-resolution genome-wide chromatin profiling, we found that a diverse set of genes can be induced to acquire locus-specific enrichment of histone H3 lysine 9 trimethylation (H3K9me3), with modification footprints extending several kilobases from the site of dsRNA homology and with locus specificity sufficient to distinguish the targeted locus from the other 20,000 genes in the C. elegans genome. Genetic analysis of the response indicated that factors responsible for secondary siRNA production during RNAi were required for effective targeting of chromatin. Temporal analysis revealed that H3K9me3, once triggered by dsRNA, can be maintained in the absence of dsRNA for at least two generations before being lost. These results implicate dsRNA-triggered chromatin modification in C. elegans as a programmable and locus-specific response defining a metastable state that can persist through generational boundaries.

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    • "The location of EERs and their potential association with heterochromatin and recombination hotspots suggests they may play a role in organization of chromatin domains and proper segregation of chromosomes. In support of this idea, small RNAs, which in some cases might derive from EERs, mediate homology-driven deposition of heterochromatin in C. elegans (Ashe et al. 2012; Buckley et al. 2012; Gu et al. 2012). In Drosophila, ADAR antagonizes heterochromatin deposition over transposable elements (Savva et al. 2013). "
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    ABSTRACT: Recent studies hint that endogenous dsRNA plays an unexpected role in cellular signaling. However, a complete understanding of endogenous dsRNA signaling is hindered by an incomplete annotation of dsRNA-producing genes. To identify dsRNAs expressed in Caenorhabditis elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered RNA editing sites, which are strictly limited to long dsRNA substrates of Adenosine Deaminases that act on RNA (ADAR). We compared two alignment algorithms for mapping both unique and repetitive reads and detected as many as 664 editing-enriched regions (EERs) indicative of dsRNA loci. EERs are visually enriched on the distal arms of autosomes and are predicted to possess strong internal secondary structures as well as sequence complementarity with other EERs, indicative of both intramolecular and intermolecular duplexes. Most EERs were associated with protein-coding genes, with ∼1.7% of all C. elegans mRNAs containing an EER, located primarily in very long introns and in annotated, as well as unannotated, 3' UTRs. In addition to numerous EERs associated with coding genes, we identified a population of prospective noncoding EERs that were distant from protein-coding genes and that had little or no coding potential. Finally, subsets of EERs are differentially expressed during development as well as during starvation and infection with bacterial or fungal pathogens. By combining RNA-seq with freely available bioinformatics tools, our workflow provides an easily accessible approach for the identification of dsRNAs, and more importantly, a catalog of the C. elegans dsRNAome. © 2015 Whipple et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
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    • "Moreover, it was recently demonstrated that the H3K9me3 signal induced by dsRNA at several loci persisted for two generations after the dsRNA induction [41]. The dsRNA-induced H3K9me3 signal was shown to spread up to 11 kb away from the dsRNA trigger region in an NRDE-2-dependent manner [41]. In addition, the germline-specific nuclear Argonaute HRDE-1/WAGO-9 has been implicated in a multigenerational germline TGS through the NRDE pathway and H3K9me [42] (see also section 4.3). "
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