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.
    RNA 03/2015; 21(5). DOI:10.1261/rna.048801.114 · 4.94 Impact Factor
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    • "Nor is it clear in many cases whether the mode of transgenerational inheritance is through the female or male germline and what groups of genes are affected. Additional studies should examine impacts of neuroendocrine disruptors on microRNAs and other non-coding RNAs such as Piwi-interacting RNA (piRNA), because they are likely to be vulnerable to changing environmental conditions in vertebrates (Zhang et al., 2010), as has been shown in Caenorhabditis elegans (Ashe et al., 2012; Gu et al., 2012b; Vandegehuchte and Janssen, 2013). Neuroendocrine disruption is more than just disturbances in hormones and feedback mechanisms. "
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    ABSTRACT: In the last few years, it has become clear that a wide variety of environmental contaminants have specific effects on neuroendocrine systems in fish, amphibians, birds and mammals. While it is beyond the scope of this review to provide a comprehensive examination of all of these neuroendocrine disruptors, we will focus on select representative examples. Organochlorine pesticides bioaccumulate in neuroendocrine areas of the brain that directly regulate GnRH neurons, thereby altering the expression of genes downstream of GnRH signaling. Organochlorine pesticides can also agonize or antagonize hormone receptors, adversely affecting crosstalk between neurotransmitter systems. The impacts of polychlorinated biphenyls are varied and in many cases subtle. This is particularly true for neuroedocrine and behavioral effects of exposure. These effects impact sexual differentiation of the hypothalamic-pituitary-gonadal axis, and other neuroendocrine systems regulating the thyroid, metabolic, and stress axes and their physiological responses. Weakly estrogenic and anti-androgenic pollutants such as bisphenol A, phthalates, phytochemicals, and the fungicide vinclozolin can lead to severe and widespread neuroendocrine disruptions in discrete brain regions, including the hippocampus, amygdala, and hypothalamus, resulting in behavioral changes in a wide range of species. Behavioral features that have been shown to be affected by one or more these chemicals include cognitive deficits, heightened anxiety or anxiety-like, sociosexual, locomotor, and appetitive behaviors. Neuroactive pharmaceuticals are now widely detected in aquatic environments and water supplies through the release of wastewater treatment plant effluents. The antidepressant fluoxetine is one such pharmaceutical neuroendocrine disruptor. Fluoxetine is a selective serotonin reuptake inhibitor that can affect multiple neuroendocrine pathways and behavioral circuits, including disruptive effects on reproduction and feeding in fish. There is growing evidence for the association between environmental contaminant exposures and diseases with strong neuroendocrine components, for example decreased fecundity, neurodegeneration, and cardiac disease. It is critical to consider the timing of exposures of neuroendocrine disruptors because embryonic stages of central nervous system development are exquisitely sensitive to adverse effects. There is also evidence for epigenetic and transgenerational neuroendocrine disrupting effects of some pollutants. We must now consider the impacts of neuroendocrine disruptors on reproduction, development, growth and behaviors, and the population consequences for evolutionary change in an increasingly contaminated world. This review examines the evidence to date that various so-called neuroendocrine disruptors can induce such effects often at environmentally-relevant concentrations.
    General and Comparative Endocrinology 02/2014; 203. DOI:10.1016/j.ygcen.2014.02.005 · 2.47 Impact Factor
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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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    ABSTRACT: The role of RNA interference (RNAi) in post-transcriptional regulation of complementary targets is well known. However, less is known about transcriptional silencing mechanisms mediated by RNAi. Such mechanisms have been characterized in yeast and plants, which suggests that similar RNA silencing mechanisms might operate in animals. A growing amount of experimental evidence indicates that short RNAs and their co-factor Argonaute proteins can regulate many nuclear processes in metazoans. PIWI-interacting RNAs (piRNAs) initiate transcriptional silencing of transposable elements, which leads to heterochromatin formation and/or DNA methylation. In addition, Argonaute proteins and short RNAs directly regulate Pol II transcription and splicing of euchromatic protein-coding genes and also affect genome architecture. Therefore, RNAi pathways can have a profound global impact on the transcriptional programs in cells during animal development. This article is part of a special issue entitled: Chromatin and epigenetic regulation of animal development. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development, edited by Dr. Peter Verrijzer and Dr. Elissa Lei.
    Biochimica et Biophysica Acta 12/2013; 1839(3). DOI:10.1016/j.bbagrm.2013.11.009 · 4.66 Impact Factor
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