Developmental DNA methyltransferase expression in the fire ant Solenopsis invicta

A role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle

Many species are threatened by climate change and must rapidly respond to survive in changing environments. Epigenetic modifications, such as DNA methylation, can facilitate plastic responses by regulating gene expression in response to environmental cues. Understanding epigenetic responses is therefore essential for predicting species' ability to rapidly adapt in the context of global environmental change. Here, we investigated the functional significance of different methylation-associated cellular processes on temperature-dependent life history in seed beetles, Callosobruchus maculatus Fabricius 1775 (Coleoptera: Bruchidae). We assessed changes under thermal stress in (1) DNA methyltransferase (Dnmt1 and Dnmt2) expression levels, (2) genome-wide methylation and (3) reproductive performance, with (2) and (3) following treatment with 3-aminobenzamide (3AB) and zebularine (Zeb) over two generations. These drugs are well-documented to alter DNA methylation across the tree of life. We found that Dnmt1 and Dnmt2 were expressed throughout the body in males and females, but were highly expressed in females compared with males and exhibited temperature dependence. However, whole-genome methylation did not significantly vary with temperature, and only marginally or inconclusively with drug treatment. Both 3AB and Zeb led to profound temperature-dependent shifts in female reproductive life history trade-off allocation, often increasing fitness compared with control beetles. Mismatch between magnitude of treatment effects on DNA methylation versus life history effects suggest potential of 3AB and Zeb to alter reproductive trade-offs via changes in DNA repair and recycling processes, rather than or in addition to (subtle) changes in DNA methylation. Together, our results suggest that epigenetic mechanisms relating to Dnmt expression, DNA repair and recycling pathways, and possibly DNA methylation, are strongly implicated in modulating insect life history trade-offs in response to temperature change.

Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats

Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.

Labor division of worker ants can be controlled by insulin synthesis targeted through miR-279c-5p in Solenopsis invicta (Hymenoptera: Formicidae)

BACKGROUND

In social insects, the labor division of workers is ubiquitous and controlled by genetic and environmental factors. However, how they modulate this coordinately remains poorly understood.

RESULTS

We report miR-279c-5p participation in insulin synthesis and behavioral transition by negatively regulating Rab8A in Solenopsis invicta. Eusocial specific miR-279c-5p is age-associated and highly expressed in nurse workers, and localized in the cytoplasm of neurons, where it is partly co-localized with its target, Rab8A. We determined that miR-279c-5p agomir suppressed Rab8A expression in forager workers, consequently decreasing insulin content, resulting in the behavioral shift to 'nurse-like' behaviors, while the decrease in miR-279c-5p increased Rab8A expression and increased insulin content in nurse workers, leading to the behavioral shift to 'foraging-like' behaviors. Moreover, insulin could rescue the 'foraging behavior' induced by feeding miR-279c-5p to nurse workers. The overexpression and suppression of miR-279c-5p in vivo caused an obvious behavioral transition between foragers and nurses, and insulin synthesis was affected by miR-279c-5p by regulating the direct target Rab8A.

CONCLUSION

We first report that miR-279c-5p is a novel regulator that promotes labor division by negatively regulating the target gene Rab8A by controlling insulin production in ants. This miRNA-mediated mechanism is significant for understanding the behavioral plasticity of social insects between complex factors and potentially provides new targets for controlling red imported fire ants. © 2023 Society of Chemical Industry.

The role of Dnmt1 in oocyte development

The whitefly Bemisia tabaci is a globally important crop pest that is difficult to manage through current commercially available methods. While RNA interference (RNAi) is a promising strategy for managing this pest, effective target genes remain unclear. We suggest DNA methyltransferase 1 (Dnmt1) as a potential target gene due to its effect on fecundity in females in other taxa of insects. We investigated the role of Dnmt1 in B. tabaci using RNAi and immunohistochemistry to confirm its potential conserved function in insect reproduction, which will define its usefulness as a target gene. Using RNAi to downregulate Dnmt1 in female B. tabaci, we show that Dnmt1 indeed has a conserved role in reproduction, as knockdown interfered with oocyte development. Females in which Dnmt1 was knocked down had greatly reduced fecundity and fertility; this supports Dnmt1 as a suitable target gene for RNAi-mediated pest management of B. tabaci.

DNMT1 mutant ants develop normally but have disrupted oogenesis

Although DNA methylation is an important gene regulatory mechanism in mammals, its function in arthropods remains poorly understood. Studies in eusocial insects have argued for its role in caste development by regulating gene expression and splicing. However, such findings are not always consistent across studies, and have therefore remained controversial. Here we use CRISPR/Cas9 to mutate the maintenance DNA methyltransferase DNMT1 in the clonal raider ant, Ooceraea biroi. Mutants have greatly reduced DNA methylation, but no obvious developmental phenotypes, demonstrating that, unlike mammals, ants can undergo normal development without DNMT1 or DNA methylation. Additionally, we find no evidence of DNA methylation regulating caste development. However, mutants are sterile, whereas in wild-type ants, DNMT1 is localized to the ovaries and maternally provisioned into nascent oocytes. This supports the idea that DNMT1 plays a crucial but unknown role in the insect germline.

miR-22 Suppresses EMT by Mediating Metabolic Reprogramming in Colorectal Cancer through Targeting MYC-Associated Factor X

Colorectal cancer (CRC) is one of the most frequent gastrointestinal cancers. MicroRNAs (miRNAs) have been proved to be unusually expressed in CRC progression and thus alter multiple pathological processes in CRC cells. However, the specific roles and mechanisms of miR-22 in CRC have not been clearly reported. MicroRNA-22 (miR-22) and MYC-associated factor X (MAX) expressions were determined by RT-qPCR in CRC tissues and cells. The targeted regulatory effects of miR-22 and MAX were confirmed by luciferase reporter and coimmunoprecipitation assays. Also, gain- and loss-of-function and rescue experiments were used to elucidate the function and mechanism of miR-22 and MAX in CRC cells and the mouse xenograft model. We discovered that miR-22 was hypermethylated and downregulated, while MAX was upregulated in CRC. miR-22 markedly inhibited migration, invasion, glycolysis, and cancer stem cell transcription factors in CRC cells. In addition, it was found that miR-22 can directly target MAX. Additional functional experiments confirmed that MAX overexpression can rescue the effects of miR-22 on the behavior of CRC cells. This study suggested that miR-22, as a cancer suppressor, participates in CRC progression by targeting MAX, which might provide basic information for therapeutic targets for CRC.

DNA Methyltransferases: From Evolution to Clinical Applications

DNA methylation is an epigenetic mark that living beings have used in different environments. The MTases family catalyzes DNA methylation. This process is conserved from archaea to eukaryotes, from fertilization to every stage of development, and from the early stages of cancer to metastasis. The family of DNMTs has been classified into DNMT1, DNMT2, and DNMT3. Each DNMT has been duplicated or deleted, having consequences on DNMT structure and cellular function, resulting in a conserved evolutionary reaction of DNA methylation. DNMTs are conserved in the five kingdoms of life: bacteria, protists, fungi, plants, and animals. The importance of DNMTs in whether methylate or not has a historical adaptation that in mammals has been discovered in complex regulatory mechanisms to develop another padlock to genomic insurance stability. The regulatory mechanisms that control DNMTs expression are involved in a diversity of cell phenotypes and are associated with pathologies transcription deregulation. This work focused on DNA methyltransferases, their biology, functions, and new inhibitory mechanisms reported. We also discuss different approaches to inhibit DNMTs, the use of non-coding RNAs and nucleoside chemical compounds in recent studies, and their importance in biological, clinical, and industry research.

Role of the foraging gene in worker behavioral transition in the red imported fire ant, Solenopsis invicta (Hymenoptera: Formicidae)

BACKGROUND

Worker division of labor is predominant in social insects. The foraging (for) gene, which encodes cGMP-dependent protein kinase (PKG), has been implicated in the regulation of behavioral transitions in honeybees, but information regarding its function in other social insects is scarce.

RESULTS

We investigated the role of the for (Sifor) gene in the red imported fire ant, Solenopsis invicta, and found that Sifor and PKG exhibited different expression patterns in different castes, body sizes, ages and tissues of fire ants, especially in foragers and nurses. Foragers displayed greater locomotor activity but showed no preference for larval or adult odors, whereas nurses showed lesser locomotor activity but had a strong preference for larval odors. We found that the expression of Sifor was significantly higher in the heads of foragers (compared to nurses). RNA interference-mediated Sifor knockdown in foraging workers induced behavioral transition of foragers toward the nurse phenotype characterized by reduced locomotor activity and a stronger preference for larval odors. By contrast, treating nurses with 8-Br-cGMP, an activator of PKG, resulted in behavioral transition toward the forager phenotype characterized by higher locomotor activity but reduced preference for larval odors.

CONCLUSION

Our results suggest that Sifor plays a critical role in the behavioral transition between foragers and nurses of workers, which may be a promising target for RNAi-based management of worker caste organization in S. invicta. © 2022 Society of Chemical Industry.

Tools and applications for integrative analysis of DNA methylation in social insects

DNA methylation is a common epigenetic signalling tool and an important biological process which is widely studied in a large array of species. The presence, level and function of DNA methylation vary greatly across species. In some insects, DNA methylation systems are minimal, and overall methylation rates tend to be low in all studied insect species. Low methylation levels probed by whole-genome bisulphite sequencing require great care with respect to data quality control and interpretation. Here, we introduce BWASP/R, a complete workflow that allows efficient, scalable and entirely reproducible analyses of raw DNA methylation sequencing data. Consistent application of quality control filters and analysis parameters provides fair comparisons among different studies and an integrated view of all experiments on one species. We describe the capabilities of the BWASP/R workflow by re-analysing several publicly available social insect WGBS data sets, comprising 70 samples and cumulatively 147 replicates from four different species. We show that the CpG methylome comprises only about 1.5% of CpG sites in the honeybee genome and that the cumulative data are consistent with genetic signatures of site accessibility and physiological control of methylation levels.

DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

The presence of DNA methylation marks within genic intervals, also called gene body methylation, is an evolutionarily-conserved epigenetic hallmark of animal and plant methylomes. In social insects, gene body methylation is thought to contribute to behavioural plasticity, for example between foragers and nurse workers, by modulating gene expression. However, recent studies have suggested that the majority of DNA methylation is sequence-specific, and therefore cannot act as a flexible mediator between environmental cues and gene expression. To address this paradox, we examined whole-genome methylation patterns in the brains and ovaries of young honey bee workers that had been subjected to divergent social contexts: the presence or absence of the queen. Although these social contexts are known to bring about extreme changes in behavioral and reproductive traits through differential gene expression, we found no significant differences between the methylomes of workers from queenright and queenless colonies. In contrast, thousands of regions were differentially methylated between colonies, and these differences were not associated with differential gene expression in the subset of genes examined. Methylation patterns were highly similar between brain and ovary tissues and only differed in nine regions. These results strongly indicate that DNA methylation is not a driver of differential gene expression between tissues or behavioral morphs. Finally, despite the lack of difference in methylation patterns, queen presence affected the expression of all four DNA methyltransferase genes, suggesting that these enzymes have roles beyond DNA methylation. Therefore, the functional role of DNA methylation in social insect genomes remains an open question.

A review on the DNA methyltransferase family of insects: Aspect and prospects

The DNA methyltransferase family contains a conserved set of DNA-modifying enzymatic proteins. They are responsible for epigenetic gene modulation, such as transcriptional silencing, transcription activation, and post-transcriptional modulation. Recent research has revealed that the canonical DNA methyltransferases (DNMTs) biological roles go beyond their traditional functions of establishing and maintaining DNA methylation patterns. Although a complete DNA methylation toolkit is absent in most insect orders, recent evidence indicates the de novo DNA methylation and maintenance function remain conserved. Studies using various molecular approaches provided evidence that DNMTs are multi-functional proteins. However, still in-depth studies on their biological role lack due to the least studied area in insects. Here, we review the DNA methylation toolkit of insects, focusing on recent research on various insect orders, which exhibit DNA methylation at different levels, and for which DNMTs functional studies have become available in recent years. We survey research on the potential roles of DNMTs in the regulation of gene transcription in insect species. DNMTs participate in different physiological processes by interacting with other epigenetic factors. Future studies on insect's DNMTs will benefit to understand developmental processes, responses to various stimuli, and adaptability of insects to different environmental conditions.

Interacting C/EBPg and YBP regulate DNA methyltransferase 1 expression in Bombyx mori embryos and ovaries

DNA methylation is an important epigenetic modification. DNA methyltransferases (Dnmts), which catalyze the formation of 5-methylcytosine, play a role in ovarian and embryonic development in some insects. However, the underlying mechanism of Dnmt in mediating ovarian and embryonic development remains unclear. In this study, the regulation and function of Bombyx mori Dnmt1 were investigated. By progressively deleting the sequence upstream of Dnmt1, a region located between -580 and -560 region from the transcription initiation site was found to have the most transcriptional activity. Electrophoretic mobility shift assay and chromatin immunoprecipitation demonstrated that transcription factor Y box binding protein (YBP), a homolog of human Y box binding protein 1 (YBX1), bound to the -580 to -560 region. YBP knockdown and overexpression in a Bombyx cell line indicated that YBP activates Dnmt1 expression. Furthermore, GST-pulldown and co-immunoprecipitation demonstrated that YBP and ovarian CCAAT/enhancer binding protein (C/EBPg) could bind each other. Simultaneous knockdown of C/EBPg and YBP was more effective than single-gene RNAi in inhibiting Dnmt1 expression and reducing the hatching rate. These results demonstrated that the interaction of C/EBPg and YBP activated Dnmt1 expression. Correlated with the expression profiles of the studies genes, our results suggest that high-level expression and interaction of C/EBPg and YBP in ovaries and embryos enhance the expression of Dnmt1, thus ensuring high reproduction rate in B. mori.

(Epi)Genetic Mechanisms Underlying the Evolutionary Success of Eusocial Insects

Eusocial insects, such as bees, ants, and wasps of the Hymenoptera and termites of the Blattodea, are able to generate remarkable diversity in morphology and behavior despite being genetically uniform within a colony. Most eusocial insect species display caste structures in which reproductive ability is possessed by a single or a few queens while all other colony members act as workers. However, in some species, caste structure is somewhat plastic, and individuals may switch from one caste or behavioral phenotype to another in response to certain environmental cues. As different castes normally share a common genetic background, it is believed that much of this observed within-colony diversity results from transcriptional differences between individuals. This suggests that epigenetic mechanisms, featured by modified gene expression without changing genes themselves, may play an important role in eusocial insects. Indeed, epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs, have been shown to influence eusocial insects in multiple aspects, along with typical genetic regulation. This review summarizes the most recent findings regarding such mechanisms and their diverse roles in eusocial insects.

The essential role of Dnmt1 in gametogenesis in the large milkweed bug Oncopeltus fasciatus

Given the importance of DNA methylation in protection of the genome against transposable elements and transcriptional regulation in other taxonomic groups, the diversity in both levels and patterns of DNA methylation in the insects raises questions about its function and evolution. We show that the maintenance DNA methyltransferase, DNMT1, affects meiosis and is essential to fertility in milkweed bugs, Oncopeltus fasciatus, while DNA methylation is not required in somatic cells. Our results support the hypothesis that Dnmt1 is required for the transition of germ cells to gametes in O. fasciatus and that this function is conserved in male and female gametogenesis. They further suggest that DNMT1 has a function independent of DNA methylation in germ cells. Our results raise thequestion as to how a gene that is so critical to fitness across multiple insect species is able to diverge widely across the insect tree of life.

Identification of DNA (de)methylation-related genes and their transcriptional response to environmental challenges in an invasive model ascidian

Marine invasive species are constantly challenged by acute or recurring environmental stresses during their range expansions. DNA methylation-mediated stress memory has been proposed to effectively affect species' response and enhance their overall performance in recurring environmental challenges. In order to further test this proposal in marine invasive species, we identified genes in the DNA methylation and demethylation processes in the highly invasive model species, Ciona robusta, and subsequently investigated the expression patterns of these genes under recurring salinity stresses. After a genome-wide comprehensive survey, we found a total of six genes, including two genes of DNA methyltransferase 3a (DNMT3a1 and DNMT3a2), and one gene of DNA methyltransferase 1 (DNMT1), methyl-CpG-binding domain protein 2 (MBD2), methyl-CpG-binding domain protein 4 (MBD4) and ten-eleven-translocation protein 1 (TET1). Phylogenetic reconstruction and domain arrangement analyses showed that the deduced proteins of the identified genes were evolutionarily conserved and functionally similar with their orthologs. All genes were constitutively expressed in all four tested tissues. Interestingly, we found time-dependent and stress-specific gene expression patterns under high and low salinity stresses. Under the recurring high salinity stresses, DNMT3a1 and TET1 conformed to the definition of memory genes, while under the recurring low salinity stresses, two DNMT3a paralogues were identified as the memory genes. Altogether, our results clearly showed that the transcriptional patterns of (de)methylation-related genes were significantly influenced by environmental stresses, and the transcriptional memory of some (de)methylation-related genes should play crucial roles in DNA methylation-mediated stress memory during the process of biological invasions.

DNA methyltransferase 3 participates in behavioral phase change in the migratory locust

DNA methylation plays important roles in the behavioral plasticity of animals. The migratory locust, Locusta migratoria, displays striking density-dependent phenotypic plasticity that can reversely transit between solitarious and gregarious phases. However, the role and the mechanism through which DNA methylation is involved in locust phase change remain unknown. Here, we investigated the expression levels of three DNA methyltransferase genes and their roles in the regulation of locust phase changes. All three Dnmt genes, namely, Dnmt1, Dnmt2 and Dnmt3 showed high expression levels in the brains of gregarious locusts. By contrast, only Dnmt3 transcript rapidly responded to population density changes, decreasing during the isolation of gregarious locusts and steadily increasing upon the crowding of solitarious locusts. Dnmt3 knockdown significantly reduced the phase-related locomotor activity, rather than the attraction index, in gregarious and crowded solitarious locusts. Transcriptome analysis showed that Dnmt3 knockdown upregulated the genes related to metabolism and transporting activity and downregulated those associated with oxidative stress response. The expression level of the phase-core transcriptional factor, hormone receptor HR3, was significantly suppressed in the brain after Dnmt3 knockdown. Moreover, there was significant overlap in the differentially expressed genes between Dnmt3 RNAi and HR3 RNAi data sets, suggesting HR3 may act as key transcriptional factor mediating Dnmt3-controlled gene expression profiles in locust brains. These findings suggest that Dnmt3 transcription is involved in locust behavioral transition, implying the possible roles of DNA methylation in phase-related phenotypic plasticity in locusts.

Transcriptomic analysis of epigenetic modification genes in the termite Reticulitermes speratus

Eusocial insects display a caste system in which different castes are morphologically and physiologically specialized for different tasks. Recent studies have revealed that epigenetic modifications, including DNA methylation and histone modification, mediate caste determination and differentiation, longevity, and polyethism in eusocial insects. Although there has been a growing interest in the relationship between epigenetic mechanisms and phenotypic plasticity in termites, there is little information about differential expression levels among castes and expression sites for these genes in termites. Here we show royal-tissue-specific expression of epigenetic modification genes in the termite Reticulitermes speratus. Using RNA-seq, we identified 74 genes, including three DNA methyltransferases, seven sirtuins, 48 Trithorax group proteins, and 16 Polycomb group proteins. Among these genes, 15 showed king-specific expression, and 52 showed age-dependent differential expression in kings and queens. Quantitative real-time PCR revealed that DNA methyltransferase 3 is expressed specifically in the king's testis and fat body, whereas some histone modification genes are remarkably expressed in the king's testis and queen's ovary. These findings imply that epigenetic modification plays important roles in the gamete production process in termite kings and queens.

Silencing of the DNA methyltransferase 1 associated protein 1 (DMAP1) gene in the invasive ladybird Harmonia axyridis implies a role of the DNA methyltransferase 1-DMAP1 complex in female fecundity

The invasive harlequin ladybird Harmonia axyridis is a textbook example of polymorphism and polyphenism as the temperature during egg development determines the frequency of melanic morphs and the number and size of black spots in nonmelanic morphs. Recent concepts in evolutionary biology suggest that epigenetic mechanisms can translate environmental stimuli into heritable phenotypic changes. To investigate whether epigenetic mechanisms influence the penetrance and expressivity of colour morphs in H. axyridis, we used RNA interference to silence key enzymes required for DNA methylation and histone modification. We found that neither of these epigenetic mechanisms affected the frequency of different morphs, but there was a significant impact on life-history traits such as longevity and fecundity. Strikingly, we found that silencing the gene encoding for DNA methyltransferase 1 associated protein 1 (DMAP1) severely reduced female fecundity, which correlated with an abundance of degenerated ovaries in DMAP1-knockdown female beetles. Finally, we observed significant differences in DMAP1 expression when we compared native and invasive H. axyridis populations with a biocontrol strain differing in egg-laying capacity, suggesting that the DNA methyltransferase 1-DMAP1 complex may influence the invasive performance of this ladybird.

Molecular characterization of DNA methyltransferase 1 and its role in temperature change of armyworm Mythimna separata Walker

DNA methylation refers to the addition of cytosine residues in a CpG context (5'-cytosine-phosphate-guanine-3'). As one of the most common mechanisms of epigenetic modification, it plays a crucial role in regulating gene expression and in a diverse range of biological processes across all multicellular organisms. The relationship between temperature and DNA methylation and how it acts on the adaptability of migratory insects remain unknown. In the present work, a 5,496 bp full-length complementary DNA encoding 1,436 amino acids (named MsDnmt1) was cloned from the devastating migratory pest oriental armyworm, Mythimna separata Walker. The protein shares 36.8-84.4% identity with other insect Dnmt1 isoforms. Spatial and temporal expression analysis revealed that MsDnmt1 was highly expressed in adult stages and head tissue. The changing temperature decreased the expression of MsDnmt1 in both high and low temperature condition. Besides, we found that M. separata exhibited the shortest duration time from the last instar to pupae under 36°C environment when injected with DNA methylation inhibitor. Therefore, our data highlight a potential role for DNA methylation in thermal resistance, which help us to understand the biological role adaptability and colonization of migratory pest in various environments.

DNA Methylation Is Correlated with Gene Expression during Diapause Termination of Early Embryonic Development in the Silkworm (Bombyx mori)

DNA modification is a naturally occurring DNA modification in prokaryotic and eukaryotic organisms and is involved in several biological processes. Although genome-wide methylation has been studied in many insects, the understanding of global and genomic DNA methylation during insect early embryonic development, is lacking especially for insect diapause. In this study, we analyzed the relationship between DNA methylomes and transcriptomes in diapause-destined eggs compared to diapause-terminated eggs in the silkworm, Bombyx mori (B. mori). The results revealed that methylation was sparse in this species, as previously reported. Moreover, methylation levels in diapause-terminated eggs (HCl-treated) were 0.05% higher than in non-treated eggs, mainly due to the contribution of CG methylation sites. Methylation tends to occur in the coding sequences and promoter regions, especially at transcription initiation sites and short interspersed elements. Additionally, 364 methylome- and transcriptome-associated genes were identified, which showed significant differences in methylation and expression levels in diapause-destined eggs when compared with diapause-terminated eggs, and 74% of methylome and transcriptome associated genes showed both hypermethylation and elevated expression. Most importantly, Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses showed that methylation may be positively associated with Bombyx mori embryonic development, by regulating cell differentiation, metabolism, apoptosis pathways and phosphorylation. Through analyzing the G2/M phase-specific E3 ubiquitin-protein ligase (G2E3), we speculate that methylation may affect embryo diapause by regulating the cell cycle in Bombyx mori. These findings will help unravel potential linkages between DNA methylation and gene expression during early insect embryonic development and insect diapause.

Implication for DNA methylation involved in the host transfer of diamondback moth, Plutella xylostella (L.)

DNA methylation exerts extensive impacts on gene expression of various living organisms exposed to environmental variation. However, little is known whether DNA methylation is involved in the host transfer of diamondback moth, Plutella xylostella (L.), a worldwide destructive pest of crucifers. In this study, we found that P. xylostella genome exhibited a relatively low level of DNA methylation on the basis of the CpG O/E prediction and experimental validation. A significant positive linear correlation was observed between the stage-specific expressions of PxDNMT1 and DNA methylation levels (5mC content). Particularly, high levels of DNA methylation and gene expression of PxDNMT1 were observed in eggs and mature females of P. xylostella. After host transfer of P. xylostella from Raphanus sativus to Arabidopsis thaliana, we identified some potential genomic loci that might have changed methylation levels. Using the method of fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP), we also found the corresponding genes primarily involved in neural system and signaling. The expressions of six candidate genes were verified by qRT-PCR. One of the genes, Px009600, might be regulated by a DNA methylation-mediated mechanism in response to host transfer. Our study provides evidence for a functional system of DNA methylation in P. xylostella and its possible role in adaptation during host transfer. Further studies should examine methylation as responsive factors to different host plants and environmental cues in insect pests.

Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect

Social insects provide systems for studying epigenetic regulation of phenotypes, particularly with respect to differentiation of reproductive and worker castes, which typically arise from a common genetic background. The role of gene expression in caste specialization has been extensively studied, but the role of DNA methylation remains controversial. Here, we perform well replicated, integrated analyses of DNA methylation and gene expression in brains of an ant (Formica exsecta) with distinct female castes using traditional approaches (tests of differential methylation) combined with a novel approach (analysis of co-expression and co-methylation networks). We found differences in expression and methylation profiles between workers and queens at different life stages, as well as some overlap between DNA methylation and expression at the functional level. Large portions of the transcriptome and methylome are organized into "modules" of genes, some significantly associated with phenotypic traits of castes and developmental stages. Several gene co-expression modules are preserved in co-methylation networks, consistent with possible regulation of caste-specific gene expression by DNA methylation. Surprisingly, brain co-expression modules were highly preserved when compared with a previous study that examined whole-body co-expression patterns in 16 ant species, suggesting that these modules are evolutionarily conserved and for specific functions in various tissues. Altogether, these results suggest that DNA methylation participates in regulation of caste specialization and age-related physiological changes in social insects.

DNA methyltransferase BmDnmt1 and BmDnmt2 in silkworm (Bombyx mori) and the regulation of silkworm embryonic development

DNA methylation is one of the most widespread epigenetic marks and has been linked to insect development, especially influencing embryonic development. However, the regulation of DNA methylation in silkworm embryonic development and diapause remain to investigate. In this study, reverse-transcription quantitative polymerase chain reaction was performed to identify the expression level of Bombyx mori DNA methyltransferases (BmDNMTs) 1 and 2 ( BmDnmt1 and BmDnmt2) in different tissues, different embryonic developmental stages, and different strains of the silkworm. The results showed that BmDNMTs were the most highly expressed during embryonic development, especially at early embryonic stages. In particular, the expression of BmDNMTs was significantly upregulated in diapause-terminated eggs by HCl treatment. Moreover, tissue distribution showed that BmDnmt2 was highly expressed in testis and ovary, and BmDnmt1 was highly expressed in testis. This study contributes to understanding the correlation of DNA methylation occurs with embryogenesis and gametogenesis in insect, meanwhile, it provides a research orientation to further analyze the role of DNA methylation in diapause initiation and termination in insect embryonic development.

Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus

BACKGROUND

The function of cytosine (DNA) methylation in insects remains inconclusive due to a lack of mutant and/or genetic studies.

RESULTS

Here, we provide evidence for the functional role of the maintenance DNA methyltransferase 1 (Dnmt1) in an insect using experimental manipulation. Through RNA interference (RNAi), we successfully posttranscriptionally knocked down Dnmt1 in ovarian tissue of the hemipteran Oncopeltus fasciatus (the large milkweed bug). Individuals depleted for Dnmt1, and subsequently DNA methylation, failed to reproduce. Eggs were inviable and declined in number, and nuclei structure of follicular epithelium was aberrant. Erasure of DNA methylation from gene or transposon element bodies did not reveal a direct causal link to steady-state mRNA levels in somatic cells. These results reveal an important function of Dnmt1 seemingly not contingent on directly controlling gene expression.

CONCLUSIONS

This study provides direct experimental evidence for a functional role of Dnmt1 in egg production and embryo viability and uncovers a trivial role, if any, for DNA methylation in control of gene expression in O. fasciatus.

Differential Gene Expression in Red Imported Fire Ant (Solenopsis invicta) (Hymenoptera: Formicidae) Larval and Pupal Stages

Solenopsis invicta Buren is an invasive ant species that has been introduced to multiple continents. One such area, the southern United States, has a history of multiple control projects using chemical pesticides over varying ranges, often resulting in non-target effects across trophic levels. With the advent of next generation sequencing and RNAi technology, novel investigations and new control methods are possible. A robust genome-guided transcriptome assembly was used to investigate gene expression differences between S. invicta larvae and pupae. These life stages differ in many physiological processes; of special importance is the vital role of S. invicta larvae as the colonies' "communal gut". Differentially expressed transcripts were identified related to many important physiological processes, including digestion, development, cell regulation and hormone signaling. This dataset provides essential developmental knowledge that reveals the dramatic changes in gene expression associated with social insect life stage roles, and can be leveraged using RNAi to develop effective control methods.

Social context influences the expression of DNA methyltransferase genes in the honeybee

DNA methylation is a reversible epigenetic modification that alters gene expression without altering the nucleotide sequence. Epigenetic modifications have been suggested as crucial mediators between social interactions and gene expression in mammals. However, little is known about the role of DNA methylation in the life cycle of social invertebrates. Recently, honeybees have become an attractive model to study epigenetic processes in social contexts. Although DNA methyltransferase (DNMT) enzymes responsible for DNA methylation are known in this model system, the influence of social stimuli on this process remains largely unexplored. By quantifying the expression of DNMT genes (dnmt1a, dnmt2 and dnmt3) under different demographical conditions characterized by the absence or presence of immatures and young adults, we tested whether the social context affected the expression of DNMT genes. The three DNMT genes had their expression altered, indicating that distinct molecular processes were affected by social interactions. These results open avenues for future investigations into regulatory epigenetic mechanisms underlying complex traits in social invertebrates.

Comparative Transcriptomics in Two Extreme Neopterans Reveals General Trends in the Evolution of Modern Insects

The success of neopteran insects, with 1 million species described, is associated with developmental innovations such as holometaboly and the evolution from short to long germband embryogenesis. To unveil the mechanisms underlining these innovations, we compared gene expression during the ontogeny of two extreme neopterans, the cockroach Blattella germanica (polyneopteran, hemimetabolan, and short germband species) and the fly Drosophila melanogaster (endopterygote, holometabolan, and long germband species). Results revealed that genes associated with metamorphosis are predominantly expressed in late nymphal stages in B. germanica and in the early-mid embryo in D. melanogaster. In B. germanica the maternal to zygotic transition (MZT) concentrates early in embryogenesis, when juvenile hormone factors are significantly expressed. In D. melanogaster, the MZT extends throughout embryogenesis, during which time juvenile hormone factors appear to be unimportant. These differences possibly reflect broad trends in the evolution of development within neopterans, related to the germband type and the metamorphosis mode.

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Transcriptomes of cockroaches and flies show key differences along development

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Cockroaches and flies express metamorphosis factors with distinct timings in ontogeny

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Cockroaches methylate DNA in early embryogenesis, whereas flies do not

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MZT is limited to the early embryo in cockroaches, but it extends until hatching in flies

Variation in DNA Methylation Is Not Consistently Reflected by Sociality in Hymenoptera

Changes in gene regulation that underlie phenotypic evolution can be encoded directly in the DNA sequence or mediated by chromatin modifications such as DNA methylation. It has been hypothesized that the evolution of eusocial division of labor is associated with enhanced gene regulatory potential, which may include expansions in DNA methylation in the genomes of Hymenoptera (bees, ants, wasps, and sawflies). Recently, this hypothesis garnered support from analyses of a commonly used metric to estimate DNA methylation in silico, CpG content. Here, we test this hypothesis using direct, nucleotide-level measures of DNA methylation across nine species of Hymenoptera. In doing so, we generated new DNA methylomes for three species of interest, including one solitary and one facultatively eusocial halictid bee and a sawfly. We demonstrate that the strength of correlation between CpG content and DNA methylation varies widely among hymenopteran taxa, highlighting shortcomings in the utility of CpG content as a proxy for DNA methylation in comparative studies of taxa with sparse DNA methylomes. We observed strikingly high levels of DNA methylation in the sawfly relative to other investigated hymenopterans. Analyses of molecular evolution suggest the relatively distinct sawfly DNA methylome may be associated with positive selection on functional DNMT3 domains. Sawflies are an outgroup to all ants, bees, and wasps, and no sawfly species are eusocial. We find no evidence that either global expansions or variation within individual ortholog groups in DNA methylation are consistently associated with the evolution of social behavior.

Molecular characterizations of DNA methyltransferase 3 and its roles in temperature tolerance in the whitefly, Bemisia tabaci Mediterranean

The Bemisia tabaci Mediterranean (MED) cryptic species is an invasive pest, distributed worldwide, with high ecological adaptability and thermotolerance. DNA methylation (a reversible chromatin modification) is one possible change that may occur within an organism subjected to environmental stress. To assess the effects of temperature stress on DNA methyltransferase 3 (Dnmt3) in MED, we cloned and sequenced BtDnmt3 and identified its functions in response to high and low temperatures. The full-length cDNA of BtDnmt3 was 3913 bp, with an open reading frame of 1962 bp, encoding a 73.89 kDa protein. In situ hybridization showed that BtDnmt3 was expressed mainly in the posterior region. BtDnmt3 messenger RNA expression levels were significantly down-regulated after exposure to heat shock and significantly up-regulated after exposure to cold shock. Furthermore, after feeding on double-stranded RNA specific for BtDnmt3, both heat resistance and cold resistance were significantly decreased, suggesting that BtDnmt3 is associated with thermal stress response and indicating a differential response to high- and low-temperature stress in MED. Together, these results highlight a potential role for DNA methylation in thermal resistance, which is a process important to successful invasion and colonization of an alien species in various environments.