Maintenance of Genome Integrity by Mi2 Homologs CHD-3 and LET-418 in Caenorhabditis elegans

A standard workflow for community-driven manual curation of Strongyloides genome annotations

Advances in the functional genomics and bioinformatics toolkits for Strongyloides species have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies of Strongyloides species continues to grow, publicly accessible reference genomes and associated genome annotations are critical resources for researchers. Genome annotations for multiple Strongyloides species are broadly available via the WormBase and WormBase ParaSite online repositories. However, a recent phylogenetic analysis of the receptor-type guanylate cyclase (rGC) gene family in two Strongyloides species highlights the potential for errors in a large percentage of current Strongyloides gene models. Here, we present three examples of gene annotation updates within the Strongyloides rGC gene family; each example illustrates a type of error that may occur frequently within the annotation data for Strongyloides genomes. We also extend our analysis to 405 previously curated Strongyloides genes to confirm that gene model errors are found at high rates across gene families. Finally, we introduce a standard manual curation workflow for assessing gene annotation quality and generating corrections, and we discuss how it may be used to facilitate community-driven curation of parasitic nematode biodata. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans

The chromatin organization modifier domain (chromodomain) is an evolutionally conserved motif across eukaryotic species. The chromodomain mainly functions as a histone methyl-lysine reader to modulate gene expression, chromatin spatial conformation and genome stability. Mutations or aberrant expression of chromodomain proteins can result in cancer and other human diseases. Here, we systematically tag chromodomain proteins with green fluorescent protein (GFP) using CRISPR/Cas9 technology in C. elegans. By combining ChIP-seq analysis and imaging, we delineate a comprehensive expression and functional map of chromodomain proteins. We then conduct a candidate-based RNAi screening and identify factors that regulate the expression and subcellular localization of the chromodomain proteins. Specifically, we reveal an H3K9me1/2 reader, CEC-5, both by in vitro biochemistry and in vivo ChIP assays. MET-2, an H3K9me1/2 writer, is required for CEC-5 association with heterochromatin. Both MET-2 and CEC-5 are required for the normal lifespan of C. elegans. Furthermore, a forward genetic screening identifies a conserved Arginine124 of CEC-5's chromodomain, which is essential for CEC-5's association with chromatin and life span regulation. Thus, our work will serve as a reference to explore chromodomain functions and regulation in C. elegans and allow potential applications in aging-related human diseases.

Divergent regulatory roles of NuRD chromatin remodeling complex subunits GATAD2 and CHD4 in Caenorhabditis elegans

During proteotoxic stress, a pathway known as the heat shock response is induced to maintain protein-folding homeostasis or proteostasis. Previously, we identified the Caenorhabditis elegans GATAD2 ortholog, dcp-66, as a novel regulator of the heat shock response. Here, we extend these findings to show that dcp-66 positively regulates the heat shock response at the cellular, molecular, and organismal levels. As GATAD2 is a subunit of the nucleosome remodeling and deacetylase chromatin remodeling complex, we examined other nucleosome remodeling and deacetylase subunits and found that the let-418 (CHD4) nucleosome repositioning core also regulates the heat shock response. However, let-418 acts as a negative regulator of the heat shock response, in contrast to positive regulation by dcp-66. The divergent effects of these two nucleosome remodeling and deacetylase subunits extend to the regulation of other stress responses including oxidative, genotoxic, and endoplasmic reticulum stress. Furthermore, a transcriptomic approach reveals additional divergently regulated pathways, including innate immunity and embryogenesis. Taken together, this work establishes new insights into the role of nucleosome remodeling and deacetylase subunits in organismal physiology. We incorporate these findings into a molecular model whereby different mechanisms of recruitment to promoters can result in the divergent effects of nucleosome remodeling and deacetylase subunits.

Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development

BACKGROUND

Histone deacetylase (HDAC)-1, a Class-I HDAC family member, forms three types of complexes, the nucleosome remodeling deacetylase, Sin3, and CoREST complexes with the specific corepressor components chromodomain-helicase-DNA-binding protein 3 (Mi2/CHD-3), Sin3, and REST corepressor 1 (RCOR1), respectively, in humans.

OBJECTIVE

To elucidate the functional relationships among the three transcriptional corepressors during embryogenesis.

METHODS

The activities of HDA-1, LET-418, SIN-3, and SPR-1, the homologs of HDAC-1, Mi2, Sin3, and RCOR1 in Caenorhabditis elegans during embryogenesis were investigated through measurement of relative mRNA expression levels and embryonic lethality given either gene knockdown or deletion. Additionally, the terminal phenotypes of each knockdown and mutant embryo were observed using a differential-interference contrast microscope. Finally, the functional relationships among the three corepressors were examined through genetic interactions and transcriptome analyses.

RESULTS

Here, we report that each of the corepressors LET-418, SIN-3, and SPR-1 are expressed and have essential roles in C. elegans embryonic development. Our terminal phenotype observations of single mutants further implied that LET-418, SIN-3, and SPR-1 play similar roles in promoting advancement to the middle and late embryonic stages. Combined analysis of genetic interactions and gene ontology of these corepressors indicate a prominent overlapping role among SIN-3, SPR-1, and LET-418 and between SIN-3 and SPR-1.

CONCLUSION

Our findings suggest that the class-I HDAC-1 corepressors LET-418, SIN-3, and SPR-1 may cooperatively regulate the expression levels of some genes during C. elegans embryogenesis or may have some similar roles but functioning independently within a specific cell.

DNA repair, recombination, and damage signaling

DNA must be accurately copied and propagated from one cell division to the next, and from one generation to the next. To ensure the faithful transmission of the genome, a plethora of distinct as well as overlapping DNA repair and recombination pathways have evolved. These pathways repair a large variety of lesions, including alterations to single nucleotides and DNA single and double-strand breaks, that are generated as a consequence of normal cellular function or by external DNA damaging agents. In addition to the proteins that mediate DNA repair, checkpoint pathways have also evolved to monitor the genome and coordinate the action of various repair pathways. Checkpoints facilitate repair by mediating a transient cell cycle arrest, or through initiation of cell suicide if DNA damage has overwhelmed repair capacity. In this chapter, we describe the attributes of Caenorhabditis elegans that facilitate analyses of DNA repair, recombination, and checkpoint signaling in the context of a whole animal. We review the current knowledge of C. elegans DNA repair, recombination, and DNA damage response pathways, and their role during development, growth, and in the germ line. We also discuss how the analysis of mutational signatures in C. elegans is helping to inform cancer mutational signatures in humans.

Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function

Paramutations represent directed and meiotically-heritable changes in gene regulation leading to apparent violations of Mendelian inheritance. Although the mechanism and evolutionary importance of paramutation behaviors remain largely unknown, genetic screens in maize (Zea mays) identify five components affecting 24 nucleotide RNA biogenesis as required to maintain repression of a paramutant purple plant1 (pl1) allele. Currently, the RNA polymerase IV largest subunit represents the only component also specifying proper development. Here we identify a chromodomain helicase DNA-binding 3 (CHD3) protein orthologous to Arabidopsis (Arabidopsis thaliana) PICKLE as another component maintaining both pl1 paramutation and normal somatic development but without affecting overall small RNA biogenesis. In addition, genetic tests show this protein contributes to proper male gametophyte function. The similar mutant phenotypes documented in Arabidopsis and maize implicate some evolutionarily-conserved gene regulation while developmental defects associated with the two paramutation mutants are largely distinct. Our results show that a CHD3 protein responsible for normal plant ontogeny and sperm transmission also helps maintain meiotically-heritable epigenetic regulatory variation for specific alleles. This finding implicates an intersection of RNA polymerase IV function and nucleosome positioning in the paramutation process.

Genes are switched “on” and “off” during normal development by regulating DNA accessibility within the chromosomes. How certain gene variants permanently maintain “off” states from one generation to the next remains unclear, but studies in multiple eukaryotes implicate roles for specific types of small RNAs, some of which define cytosine methylation patterns. In corn, these RNAs come from at least two RNA polymerase II-derived complexes sharing a common catalytic subunit (RPD1). Although RPD1 both controls the normal developmental switching of many genes and permanently maintains some of these “off” states across generations, how RPD1 function defines heritable DNA accessibility is unknown. We discovered that a protein (CHD3a) belonging to a group known to alter nucleosome positioning is also required to help maintain a heritable “off” state for one particular corn gene variant controlling both plant and flower color. We also found CHD3a necessary for normal plant development and sperm transmission consistent with the idea that proper nucleosome positioning defines evolutionarily-important gene expression patterns. Because both CHD3a and RPD1 maintain the heritable “off” state of a specific gene variant, their functions appear to be mechanistically linked.

Neonicotinoid-containing insecticide disruption of growth, locomotion, and fertility in Caenorhabditis elegans

Neonicotinoids, a class of insecticides structurally similar to nicotine that target biting and sucking insects, are the most widely used insecticides today, in part due to their supposed low toxicity in other organisms. However, a growing body of research has found that even low doses of neonicotinoids can induce unexpected negative effects on the physiology and survival of a wide range of non-target organisms. Importantly, no work has been done on the commercial formulations of pesticides that include imidacloprid as the active ingredient, but that also contain many other components. The present study examines the sublethal effects of "Tree and Shrub"™ ("T+S"), a commercial insecticide containing the neonicotinoid imidacloprid as its active ingredient, on Caenorhabditis elegans. We discovered that "T+S" significantly stunted the overall growth in wildtype nematodes, an effect that was exacerbated by concurrent exposure to heat stress. "T+S" also negatively impacted fecundity as measured by increased germline apoptosis, a decrease in egg-laying, and fewer viable offspring. Lastly, exposure to "T+S" resulted in degenerative changes in nicotinic cholinergic neurons in wildtype nematodes. As a whole, these findings demonstrate widespread toxic effects of neonicotinoids to critical functions in nematodes.

Gamma radiation induces life stage-dependent reprotoxicity in Caenorhabditis elegans via impairment of spermatogenesis

The current study investigated life stage, tissue and cell dependent sensitivity to ionizing radiation of the nematode Caenorhabditis elegans. Results showed that irradiation of post mitotic L4 stage larvae induced no significant effects with respect to mortality, morbidity or reproduction at either acute dose ≤6 Gy (1500 mGy·h^-1) or chronic exposure ≤15 Gy (≤100 mGy·h^-1). In contrast, chronic exposure from the embryo to the L4-young adult stage caused a dose and dose-rate dependent reprotoxicity with 43% reduction in total brood size at 6.7 Gy (108 mGy·h^-1). Systematic irradiation of the different developmental stages showed that the most sensitive life stage was L1 to young L4. Exposure during these stages was associated with dose-rate dependent genotoxic effects, resulting in a 1.8 to 2 fold increase in germ cell apoptosis in larvae subjected to 40 or 100 mGy·h^-1, respectively. This was accompanied by a dose-rate dependent reduction in the number of spermatids, which was positively correlated to the reprotoxic effect (0.99, PCC). RNAseq analysis of nematodes irradiated from L1 to L4 stage revealed a significant enrichment of differentially expressed genes related to both male and hermaphrodite reproductive processes. Gene network analysis revealed effects related to down-regulation of genes required for spindle formation and sperm meiosis/maturation, including smz-1, smz-2 and htas-1. Furthermore, the expression of a subset of 28 set-17 regulated Major Sperm Proteins (MSP) required for spermatid production was correlated (R² 0.80) to the reduction in reproduction and the number of spermatids. Collectively these observations corroborate the impairment of spermatogenesis as the major cause of gamma radiation induced life-stage dependent reprotoxic effect. Furthermore, the progeny of irradiated nematodes showed significant embryonal DNA damage that was associated with persistent effect on somatic growth. Unexpectedly, these nematodes maintained much of their reproductive capacity in spite of the reduced growth.

The Epigenetics of Aging in Invertebrates

Aging is an unstoppable process coupled to the loss of physiological function and increased susceptibility to diseases. Epigenetic alteration is one of the hallmarks of aging, which involves changes in DNA methylation patterns, post-translational modification of histones, chromatin remodeling and non-coding RNA interference. Invertebrate model organisms, such as Drosophila melanogaster and Caenorhabditis elegans, have been used to investigate the biological mechanisms of aging because they show, evolutionarily, the conservation of many aspects of aging. In this review, we focus on recent advances in the epigenetic changes of aging with invertebrate models, providing insight into the relationship between epigenetic dynamics and aging.