Burton NO et al. (2011) Proc Natl Acad Sci U S A "Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans."

Kennedy S, Burkhart KB, Burton NO

[Proc Natl Acad Sci U S A, 2011]

RNA interference (RNAi) is heritable in Caenorhabditis elegans; the progeny of C. elegans exposed to dsRNA inherit the ability to silence genes that were targeted by RNAi in the previous generation. Here we investigate the mechanism of RNAi inheritance in C. elegans. We show that exposure of animals to dsRNA results in the heritable expression of siRNAs and the heritable deposition of histone 3 lysine 9 methylation (H3K9me) marks in progeny. siRNAs are detectable before the appearance of H3K9me marks, suggesting that chromatin marks are not directly inherited but, rather, reestablished in inheriting progeny. Interestingly, H3K9me marks appear more prominently in inheriting progeny than in animals directly exposed to dsRNA, suggesting that germ-line transmission of silencing signals may enhance the efficiency of siRNA-directed H3K9me. Finally, we show that the nuclear RNAi (Nrde) pathway maintains heritable RNAi silencing in C. elegans. The Argonaute (Ago) NRDE-3 associates with heritable siRNAs and, acting in conjunction with the nuclear RNAi factors NRDE-1, NRDE-2, and NRDE-4, promotes siRNA expression in inheriting progeny. These results demonstrate that siRNA expression is heritable in C. elegans and define an RNAi pathway that promotes the maintenance of RNAi silencing and siRNA expression in the progeny of animals exposed to dsRNA.

Fisher K et al. (2010) Dev Biol "Methylation and demethylation activities of a C. elegans MLL-like complex attenuate RAS signalling."

Wilson JR, Poulin GB, Southall SM, Fisher K

[Dev Biol, 2010]

The conserved Mixed Lineage Leukaemia (MLL) complex deposits activating methyl marks on histone tails through a methyltransferase (MT) activity. Here we provide in vivo evidence that in addition to methylation, the C. elegans MLL-like complex can remove specific methyl marks linked to repression of transcription. This supports the proposed model in which the MLL complex orchestrates both the deposition and the removal of methyl marks to activate transcription. We have uncovered the MLL-like complex in a large-scale RNAi screen designed to identify attenuators of RAS signalling during vulval development. We have also found that the histone acetyltransferase complex, NuA4/TIP60, cooperates with the C. elegans MLL-like complex in the attenuation of RAS signalling. Critically, we show that both complexes regulate a common novel target and attenuator of RAS signalling, AJM-1 (Apical Junction Molecule-1). Therefore, the C. elegans MLL-like complex cooperates with the NuA4/TIP60 complex to regulate the expression of a novel effector, AJM-1.

Allo M et al. (2010) Curr Biol "Gene silencing: small RNAs control RNA polymerase II elongation."

Allo M, Kornblihtt AR

[Curr Biol, 2010]

Short interfering RNAs trigger histone silencing marks and stalling of RNA polymerase II at their genomic target sites through a mechanism termed transcriptional gene silencing (TGS). The Argonaute protein NRDE-3, along with NRDE-2, are needed for TGS in C. elegans. TGS also inhibits elongation and controls alternative splicing in mammalian cells.

Lan KY et al. (2021) Comput Struct Biotechnol J "Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals."

Liao BY, Lan KY

[Comput Struct Biotechnol J, 2021]

The results of conventional gene-based analyses which combine epigenome and transcriptome data, including those conducted by the ENCODE/modENCODE projects, suggest various histone modifications performing regulatory functions in controlling mRNA expression (referred to as a histone code) in several model animals. While some histone codes were found to be universally adopted across organisms, "species-specific" histone codes have also been defined. We found that the characterization of these histone codes was confounded by factors (e.g. gene essentiality, expression breadth) that are independent of, but correlated with, gene expression levels. Hence, we attempted to decode histone marks in mouse (<i>Mus musculus</i>), fly (<i>Drosophila melanogaster</i>), and worm (<i>Caenorhabditis elegans</i>) genomes by examining ratios of RNA sequencing (and chromatin immunoprecipitation sequencing) intensities between paralog genes to remove confounding effects that would otherwise be present in a gene-based approach. With this paralog-based approach, associations between four histone modifications (H3K4me3, H3K27ac, H3K9ac, and H3K36me3) and gene expression are substantially revised. For example, we demonstrate that H3K27ac and H3K9ac represent universal active marks in promoters, rather than worm-specific marks as previously reported. Second, acting regions of the studied active marks that are common across species (and across a wide range of tissues at different developmental stages) were found to extend beyond the previously defined regions. Thus, it appears that the active histone codes analyzed have a universality that has previously been underappreciated. Our results suggested that these universal codes, including those previously considered species-specific, could have an ancient origin, and are important in regulating animal gene expression abundance.

Maures TJ et al. (2011) Aging Cell "The H3K27 demethylase UTX-1 regulates C.elegans lifespan in a germline-independent, insulin-dependent manner."

Brunet A, Greer EL, Hauswirth AG, Maures TJ

[Aging Cell, 2011]

Aging is accompanied by alterations in epigenetic marks that control chromatin states, including histone acetylation and methylation. Enzymes that reversibly affect histone marks associated with active chromatin have recently been found to regulate aging in Caenorhabditis elegans. However, relatively little is known about the importance for aging of histone marks associated with repressed chromatin. Here, we use a targeted RNAi screen in C.elegans to identify four histone demethylases that significantly regulate worm lifespan, UTX-1, RBR-2, LSD-1, and T26A5.5. Interestingly, UTX-1 belongs to a conserved family of histone demethylases specific for lysine 27 of histone H3 (H3K27me3), a mark associated with repressed chromatin. Both utx-1 knockdown and heterozygous mutation of utx-1 extend lifespan and increase the global levels of the H3K27me3 mark in worms. The H3K27me3 mark significantly drops in somatic cells during the normal aging process. UTX-1 regulates lifespan independently of the presence of the germline, but in a manner that depends on the insulin-FoxO signaling pathway. These findings identify the H3K27me3 histone demethylase UTX-1 as a novel regulator of worm lifespan in somatic cells.

Tian Y et al. (2016) Cell "Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPR(mt)."

Wolff S, Steffen KK, Joe L, Dillin A, Garcia G, Tian Y, Bian Q, Meyer BJ

[Cell, 2016]

Organisms respond to mitochondrial stress through the upregulation of an array of protective genes, often perpetuating an early response to metabolic dysfunction across a lifetime. We find that mitochondrial stress causes widespread changes in chromatinstructure through histone H3K9 di-methylation marks traditionally associated with gene silencing. Mitochondrial stress response activation requires the di-methylation of histone H3K9 through the activity of the histone methyltransferase met-2 and the nuclear co-factor lin-65. While globally the chromatin becomes silenced by these marks, remaining portions of the chromatin open up, at which point the binding of canonical stress responsive factors such as DVE-1 occurs. Thus, a metabolic stress response is established and propagated into adulthood of animals through specific epigenetic modifications that allow for selective gene expression and lifespan extension.

Maduro MF (2015) Worm "20 Years of unc-119 as a transgene marker."

Maduro MF

[Worm, 2015]

This fall marks 20years since the cloning of unc-119 was reported. Despite having a strong phenotype that makes animals somewhat difficult to grow and handle, unc-119 mutant rescue has become one of the most frequently-used markers for C. elegans transformation. In this Commentary, I describe the history of how unc-119 rescue traveled through the worm community, contributing to the development of transgene methods in C. elegans.

Chory EJ et al. (2019) Mol Cell "Nucleosome Turnover Regulates Histone Methylation Patterns over the Genome."

Bell O, Crabtree GR, Calarco JP, Neel DS, Hathaway NA, Chory EJ

[Mol Cell, 2019]

Recent studies have indicated that nucleosome turnover is rapid, occurring several times per cell cycle. To access the effect of nucleosome turnover on theepigenetic landscape, we investigated H3K79 methylation, which is produced by a single methyltransferase (Dot1l) with no known demethylase. Using chemical-induced proximity (CIP), we find that the valency of H3K79 methylation (mono-, di-, and tri-) is determined by nucleosome turnover rates. Furthermore, propagation of this mark is predicted by nucleosome turnover simulations over the genome and accounts for the asymmetric distribution of H3K79me toward the transcriptional unit. More broadly, a meta-analysis of other conserved histone modifications demonstrates that nucleosome turnover models predict both valency and chromosomal propagation of methylation marks. Based on data from worms, flies, and mice, we propose that the turnover of modified nucleosomes is a general means of propagation of epigenetic marks and a determinant of methylation valence.

Chang AY et al. (2017) Genome Res "Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution."

Chang AY, Liao BY

[Genome Res, 2017]

Following gene duplication, mRNA expression of the duplicated gene is reduced to maintain mRNA dosage. In mammals, this process is achieved with increased cytosine DNA methylation of the promoters of duplicated genes to suppress transcriptional initiation. However, not all animal species possess a full apparatus for cytosine DNA methylation. For such species such as roundworm (Caenorhabditis elegans, &quot;worm&quot; hereafter) or fruit fly (Drosophila melanogaster, &quot;fly&quot; hereafter), it is unclear how reduced expression of duplicated genes has been achieved evolutionarily. Here, we hypothesize that in the absence of a classical cytosine DNA methylation pathway, histone modifications play an increasing role in maintaining mRNA dosage following gene duplication. We initially verified that reduced gene expression of duplicated genes had occurred in worm, fly, and mouse (Mus musculus). Next, several histone marks with the capacity to control mRNA abundance in the models studied were examined. In worm and fly, but not in mouse, multiple histone modifications were found to assist mRNA dosage maintenance following gene duplication events, and the possible involvement of adenine DNA methylation in this process was excluded. Furthermore, the histone marks and acting regions that mediated the reduction in duplicated gene expression were found to be largely organism-specific. Thus, it appears that many of the histone marks that maintain mRNA dosage were independently recruited during the evolution of worms and flies to compensate for the loss of cytosine DNA methylation machinery from their genomes.

Rudgalvyte M et al. (2016) Comp Biochem Physiol C Toxicol Pharmacol "Chronic MeHg exposure modifies the histone H3K4me3 epigenetic landscape in Caenorhabditis elegans."

Rudgalvyte M, Lakso M, Peltonen J, Wong G

[Comp Biochem Physiol C Toxicol Pharmacol, 2016]

Methylmercury (MeHg) is a persistent environmental pollutant that occurs in the food chain, at occupational sites, and via medical procedures. Exposure in humans and animal models results in renal, neuro, and reproductive toxicities. In this study, we demonstrate that chronic exposure to MeHg (10uM) causes epigenetic landscape modifications of histone H3K4 trimethylation (H3K4me3) marks in Caenorhabditis elegans using chromatin immuno-precipitation sequencing (ChIP-seq). The modifications correspond to the locations of 1467 genes with enhanced and 508 genes with reduced signals. Among enhanced genes are those encoding glutathione-S-transferases, lipocalin-related protein and a cuticular collagen. ChIP-seq enhancement of these genes was confirmed with increased mRNA expression levels revealed by qRT-PCR. Furthermore, we observed enhancement of H3K4me3 marks in these genes in animals exposed to MeHg in utero and assayed at L4 stage. In utero exposure enhanced marks without alterations in mRNA expression except for the lpr-5 gene. Finally, knockdown of lipocalin-related protein gene lpr-5, which is involved in intercellular signaling, and cuticular collagen gene dpy-7, structural component of the cuticle, by RNA interference (RNAi) resulted in increased lethality of animals after MeHg exposure. Our results provide new data on the epigenetic landscape changes elicited by MeHg exposure, as well as describe a unique model for studying in utero effects of heavy metals. Together, these findings may help to understand the toxicological effects of MeHg at the molecular level.