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

Genome-wide DNA methylation profile and its function in regulating Vip3Aa tolerance in fall armyworm (Spodoptera frugiperda)

BACKGROUND

Vegetative insecticidal proteins (Vips) are widely used in pest management, but Vip tolerance poses a significant threat. DNA methylation plays important roles in regulating the response of biological organisms to environmental stress, and it may also regulate fall armyworm (FAW, Spodoptera frugiperda) Vip3Aa tolerance.

RESULTS

In this study, a DNA methylation map was developed for FAW, and its function in regulating FAW Vip3Aa tolerance was explored. The FAW genome-wide DNA methylation map showed that exons were preferred regions for DNA methylation and housekeeping genes were highly methylated. FAW was screened using Vip3Aa for ten generations, and bioassays indicated that Vip3Aa tolerance increased trans-generationally. A comparison of DNA methylation maps between Vip3Aa-tolerant and -susceptible strains showed that gene body methylation was positively correlated with gene expression level. FAW exhibits significant variation in DNA methylation among individuals, and Vip3Aa screening induces epigenetic variation based on DNA methylation. Moreover, the study demonstrated that a reduction in methylation density within the gene body of a 3'5'-cyclic nucleotide phosphodiesterase gene resulted in decreased expression and increased tolerance of FAW to Vip3Aa, which was validated through RNA interference experiments.

CONCLUSION

The DNA methylation map and mechanism of Vip3Aa tolerance improve our understanding of DNA methylation and its function in Lepidoptera and provide a new perspective for developing pest management strategies. © 2024 Society of Chemical Industry.

RNA N6-methyladenosine of DHAPAT and PAP involves in regulation of diapause of Bombyx mori via the lipid metabolism pathway

Environment-induced epigenetics are involved in diapause regulation, but the molecular mechanism that epigenetically couples nutrient metabolism to diapause regulation remains unclear. In this study, we paid special attention to the significant differences in the level of N6-adenosine methylation (m6A) of dihydroxyacetone phosphate acyltransferase (DHAPAT) and phosphatidate phosphatase (PAP) genes in the lipid metabolism pathway of the bivoltine silkworm (Bombyx mori) strain Qiufeng developed from eggs incubated at a normal temperature (QFHT, diapause egg producer) compared to those from eggs incubated at a low temperature (QFLT, non-diapause egg producer). We knocked down DHAPAT in the pupal stage of the QFLT group, resulting in the non-diapause destined eggs becoming diapausing eggs. In the PAP knockdown group, the colour of the non-diapause destined eggs changed from light yellow to pink 3 days after oviposition, but they hatched as normal. Moreover, we validated that YTHDF3 binds to m6A-modified DHAPAT and PAP mRNAs to promote their stability and translation. These results suggest that RNA m6A methylation participates in the diapause regulation of silkworm by changing the expression levels of DHAPAT and PAP and reveal that m6A epigenetic modification can be combined with a lipid metabolism signal pathway to participate in the regulation of insect diapause traits, which provides a clearer image for exploring the physiological basis of insect diapause.

Comprehensive analysis of the expression, prognostic significance, and regulation pathway of G2E3 in breast cancer

BACKGROUND

Loss of G2-specific E3-like (G2E3) protein sensitizes tumor cells to chemotherapy. However, the role of G2E3 in breast cancer development and patient's prognosis is unclear. Here, we explored the expression, prognostic significance, and regulatory pathway of G2E3 in breast cancer.

METHODS

TCGA and UALCAN database were utilized to explore G2E3 expression in breast cancer and normal tissues and its expression in breast cancer based on clinicopathological characteristics, respectively. The Kaplan-Meier plotter database was utilized to determine the effect of G2E3 on the prognosis of breast cancer patients. RT-PCR was utilized to validate the G2E3 expression in cancerous and normal breast tissues. Immunohistochemistry analysis was utilized to validate the prognostic effect of G2E3 expression in breast cancer patients and the relationship between G2E3 expression and lymphocyte infiltration levels. Receiver operating characteristic (ROC) curves were also generated to validate the diagnostic value of G2E3 expression in recurrence/distant organ metastasis and death. The STRING database, DAVID database, and Sanger-box tools were utilized to perform GO functional, KEGG pathway enrichment, and GSEA analysis. The TISIDB database was utilized to determine the relationship between G2E3 expression and tumor immunity. Finally, CTD database was utilized to screen for potential therapeutic compounds that could reduce the G2E3 mRNA expression.

RESULTS

TCGA data presented that G2E3 expression was higher in breast cancer tissues than in normal breast tissues. This result was further validated by RT-PCR (P = 0.003). The Kaplan-Meier plotter database suggested that patients with high G2E3 mRNA expression had significantly shorter RFS and OS than patients with low G2E3 mRNA expression. Immunohistochemistry analysis of 156 breast cancer clinical specimens also validated patients with G2E3-positive expression had a significantly shorter DFS and OS than patients with G2E3-negative expression. Thus, G2E3 expression was an independent prognostic predictor of DFS and OS. The G2E3-positive expression also has a high diagnostic value for recurrence/distant organ metastasis and death. GSEA analysis revealed that G2E3 might be enriched in the E2F, PI3K/AKT/mTOR signaling, DNA repair pathways, and other cancer-related signaling pathways. The TISIDB database showed that G2E3 expression was significantly negatively associated with lymphocyte infiltration. This result was further validated in clinical breast cancer samples (P = 0.048; R = -0.158). Using the CTD database, we found that (+)-JQ1 compound, 1,2-dimethylhydrazine, and other compounds may decrease the G2E3 mRNA expression. These compounds could serve as potential therapeutic compounds for the clinical treatment of breast cancer.

CONCLUSIONS

G2E3 expression was higher in breast cancer tissues than in normal tissues. G2E3-positive expression was related to a worse survival outcome in patients with breast cancer. Genes co-expressed with G2E3 may be enriched in the breast cancer-related signaling pathways. The G2E3 expression was significantly negatively associated with lymphocyte infiltration. G2E3 may serve as a novel prognostic biomarker and therapeutic target for breast cancer.

Dynamic transcriptome analysis of Bombyx mori embryonic development

Bombyx mori has been extensively studied but the gene expression control of its embryonic development is unclear. In this study, we performed transcriptome profiling of six stages of B. mori embryonic development using RNA sequencing (RNA-seq). A total of 12 894 transcripts were obtained from the embryos. Of these, 12 456 transcripts were shared among the six stages, namely, fertilized egg, blastoderm, germ-band, organogenesis, reversal period, and youth period stages. There were 111, 48, 41, 54, 77, and 107 transcripts specifically expressed during the six stages, respectively. By analyzing weighted gene correlation networks and differently expressed genes, we found that during embryonic development, many genes related to DNA replication, transcription, protein synthesis, and epigenetic modifications were upregulated in the early embryos. Genes of cuticle proteins, chitin synthesis-related proteins, and neuropeptides were more abundant in the late embryos. Although pathways of juvenile hormone and the ecdysteroid 20-hydroxyecdysone, and transcription factors were expressed throughout the embryonic development stages, more regulatory pathways were highly expressed around the organogenesis stage, suggesting more gene expression for organogenesis. The results of RNA-seq were confirmed by quantitative real-time polymerase chain reaction of 16 genes of different pathways. Nucleic acid methylation and seven sites in histone H3 modifications were confirmed by dot blot and western blot. This study increases the understanding of the molecular mechanisms of the embryonic developmental process and information on the regulation of B. mori development.

Transcriptional Regulation of Reproductive Diapause in the Convergent Lady Beetle, Hippodamia convergens

Simple Summary

Diapause is a dormant period typically controlled by daylength that ensures an insect’s survival through harsh environmental conditions. The convergent lady beetle, Hippodamia convergens, undergoes a reproductive diapause in winter, where female ovaries remain immature and no eggs are laid. This species is an important biological control agent, but during diapause, beetles are less likely to eat pest insects. Thus, knowledge of diapause mechanisms may facilitate manipulation thereof to improve biological control. Further, molecular studies of adult diapause and diapause in Coleoptera are relatively lacking. Here, we assembled and annotated a transcriptome for this species and quantified transcript expression changes during diapause. Female beetles were sampled at three times in diapause (early, mid, and late diapause), which allowed us to characterize the molecular processes occurring at distinct transitions throughout diapause. We found that transcripts involved in flight were consistently upregulated during diapause, which is consistent with dispersal flights at this stage, while transcripts involved in ovarian development were downregulated, which is consistent with the shutdown of reproduction in diapausing females. These findings identify key regulators of diapause in H. convergens and contribute to a growing body of literature on the molecular mechanisms of diapause across the insect phylogeny.

Abstract

Diapause is an alternate development program that synchronizes an insect’s life cycle with seasonally abundant resources and ensures survival in unfavorable conditions. The physiological basis of diapause has been well characterized, but the molecular mechanisms regulating it are still being elucidated. Here, we present a de novo transcriptome and quantify transcript expression during diapause in the convergent lady beetle Hippodamia convergens. H. convergens is used as an augmentative biocontrol agent, and adult females undergo reproductive diapause that is regulated by photoperiod. We sampled females at three stages (early, mid, and late diapause) and compared transcript expression to non-diapausing individuals. Based on principle component analysis, the transcriptomes of diapausing beetles were distinct from non-diapausing beetles, and the three diapausing points tended to cluster together. However, there were still classes of transcripts that differed in expression across distinct phases of diapause. In general, transcripts involved in muscle function and flight were upregulated during diapause, likely to support dispersal flights that occur during diapause, while transcripts involved in ovarian development were downregulated. This information could be used to improve biological control by manipulating diapause. Additionally, our data contribute to a growing understanding of the genetic regulation of diapause across diverse insects.

Changes in gene body methylation do not correlate with changes in gene expression in Anthozoa or Hexapoda

Background

As human activity alters the planet, there is a pressing need to understand how organisms adapt to environmental change. Of growing interest in this area is the role of epigenetic modifications, such as DNA methylation, in tailoring gene expression to fit novel conditions. Here, we reanalyzed nine invertebrate (Anthozoa and Hexapoda) datasets to validate a key prediction of this hypothesis: changes in DNA methylation in response to some condition correlate with changes in gene expression.

Results

In accord with previous observations, baseline levels of gene body methylation (GBM) positively correlated with transcription, and negatively correlated with transcriptional variation between conditions. Correlations between changes in GBM and transcription, however, were negligible. There was also no consistent negative correlation between methylation and transcription at the level of gene body methylation class (either highly- or lowly-methylated), anticipated under the previously described “seesaw hypothesis”.

Conclusion

Our results do not support the direct involvement of GBM in regulating dynamic transcriptional responses in invertebrates. If changes in DNA methylation regulate invertebrate transcription, the mechanism must involve additional factors or regulatory influences.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08474-z.

Phenotypic Plasticity: What Has DNA Methylation Got to Do with It?

How does one genome give rise to multiple, often markedly different, phenotypes in response to an environmental cue? This phenomenon, known as phenotypic plasticity, is common amongst plants and animals, but arguably the most striking examples are seen in insects. Well-known insect examples include seasonal morphs of butterfly wing patterns, sexual and asexual reproduction in aphids, and queen and worker castes of eusocial insects. Ultimately, we need to understand how phenotypic plasticity works at a mechanistic level; how do environmental signals alter gene expression, and how are changes in gene expression translated into novel morphology, physiology and behaviour? Understanding how plasticity works is of major interest in evolutionary-developmental biology and may have implications for understanding how insects respond to global change. It has been proposed that epigenetic mechanisms, specifically DNA methylation, are the key link between environmental cues and changes in gene expression. Here, we review the available evidence on the function of DNA methylation of insects, the possible role(s) for DNA methylation in phenotypic plasticity and also highlight key outstanding questions in this field as well as new experimental approaches to address these questions.

Genome assembly and methylome analysis of the white wax scale insect provides insight into sexual differentiation of metamorphosis in hexapods

Scale insects are hemimetabolous, showing "incomplete" metamorphosis and no true pupal stage. Ericerus pela, commonly known as the white wax scale insect (hereafter, WWS), is a wax-producing insect found in Asia and Europe. WWS displays dramatic sexual dimorphism, with notably different metamorphic fates in males and females. Males develop into winged adults, while females are neotenic and maintain a nymph-like appearance, which are flightless and remain stationary. Here, we report the de novo assembly of the WWS genome with a size of 638.30 Mbp (69.68 Mbp for scaffold N50) by PacBio sequencing and Hi-C. These data allowed us to perform a robust phylogenetic analysis comprising 24,923 gene orthogroups from 16 representative insect genomes. This analysis indicated that holometabola evolved from insects with incomplete metamorphosis in the Late Carboniferous, about 50 million years earlier than previously thought. To study the distinct developmental fates of males and females, we analysed the methylome landscape in either sex. Surprisingly, WWS displayed high methylation levels (4.42% for males) when compared to other insects. We observed differential methylation patterns in males and females for genes involved in steroid and sesquiterpenoid production as well as genes acting in fatty acid metabolism pathways. We measured titre profiles for ecdysone, the principal insect steroid hormone, and juvenile hormone (a sesquiterpenoid) in both males and females, which suggested that these hormones are the primary drivers of sexually dimorphic development. Our results provide a comprehensive genomic and epigenomic resource of scale insects that provide new insights into the evolution of metamorphosis and sexual dimorphism in insects.

Whole genome bisulfite sequencing methylome analysis of mulberry (Morus alba) reveals epigenome modifications in response to drought stress

DNA methylation plays a significant role in many biological processes. Although some studies of DNA methylation have been performed in woody plant, none is known about the methylation patterns of mulberry (Morus alba). In this study, we performed whole genome bisulfite sequencing under drought stress to generate a methylated cytosines map and assessed the effects of the changes on gene expression combined with transcriptomics. We found that the percentage of methylated cytosines varied depending on the local sequence context (CG, CHG and CHH) and external treatment (control, CK; drought stress, DS). The methylation levels under DS were 8.64% higher than that of CK, and differences that were mainly due to the contribution of mCG (6.24%). Additionally, there were 3,243 different methylation and expression associated genes. In addition, methylated genes were enriched within GO subcategories including catalytic activity, cellular process, metabolic process, response to stimulus and regulation of biological process. This is the first study to comprehensively present methylation patterns in mulberry and reveal widespread DNA methylation changes in response to drought stress, which has the potential to enhance our understanding of links between DNA methylation and the modulation of gene expression in plants subjected to abiotic stresses.