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Robert J Schmitz - One of the best experts on this subject based on the ideXlab platform.
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the essential role of dnmt1 in gametogenesis in the Large Milkweed Bug oncopeltus fasciatus
bioRxiv, 2020Co-Authors: Joshua T Washington, Elizabeth C Mckinney, Robert J Schmitz, Katelyn R Cavender, Ashley U Amukamara, Patricia J MooreAbstract: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 the question of how a gene so critical in fitness across multiple insect species can have diverged widely across the insect tree of life.
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dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug oncopeltus fasciatus
Epigenetics & Chromatin, 2019Co-Authors: Adam Bewick, Zachary Sanchez, Allen J Moore, Elizabeth C Mckinney, Patricia J Moore, Robert J SchmitzAbstract:The function of cytosine (DNA) methylation in insects remains inconclusive due to a lack of mutant and/or genetic studies. 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. 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.
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Dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug, Oncopeltus fasciatus
Epigenetics & Chromatin, 2019Co-Authors: Adam Bewick, Zachary Sanchez, Allen J Moore, Elizabeth C Mckinney, Patricia J Moore, Robert J SchmitzAbstract: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 .
Allen J Moore - One of the best experts on this subject based on the ideXlab platform.
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Dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug, Oncopeltus fasciatus
Epigenetics & Chromatin, 2019Co-Authors: Adam Bewick, Zachary Sanchez, Allen J Moore, Elizabeth C Mckinney, Patricia J Moore, Robert J SchmitzAbstract: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 .
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dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug oncopeltus fasciatus
Epigenetics & Chromatin, 2019Co-Authors: Adam Bewick, Zachary Sanchez, Allen J Moore, Elizabeth C Mckinney, Patricia J Moore, Robert J SchmitzAbstract:The function of cytosine (DNA) methylation in insects remains inconclusive due to a lack of mutant and/or genetic studies. 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. 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.
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chemical egg defence in the Large Milkweed Bug oncopeltus fasciatus derives from maternal but not paternal diet
Entomologia Experimentalis Et Applicata, 2013Co-Authors: Devi Newcombe, Jonathan D Blount, Christopher A Mitchell, Allen J MooreAbstract:Many herbivorous insects sequester defensive compounds from their host-plants and incorporate them into their eggs to protect them against predation. Here, we investigate whether transmission of cardenolides from the host-diet to the eggs is maternal, paternal, or biparental in the Large Milkweed Bug, Oncopeltus fasciatus (Dallas) (Hemiptera: Lygaeidae). We reared individual Bugs on either Milkweed seeds [MW; Asclepias syriaca L. (Apocynaceae)] that contain cardenolides, or on sunflower seeds [SF; Helianthus annuus L. (Asteraceae)] that do not contain cardenolides. We mated females and males so that all four maternal/paternal diet combinations were represented: MW/MW, MW/SF, SF/MW, and SF/SF. Using larvae of the common green lacewing, Chrysoperla (Chrysopa) carnea (Stevens) (Neuroptera: Chrysopidae), we conducted two-choice predation trials to assess whether maternal, paternal, or biparental transmission of cardenolides into the eggs of O. fasciatus increased protection against predation. Furthermore, we used high performance liquid chromatography (HPLC) to assess putative cardenolide content of eggs from the various parental diet treatment groups. The predation trials suggested that regardless of male diet, eggs were afforded better protection when females had been raised on Milkweed. However, many eggs were at least partially consumed. This suggests that although chemical defence of eggs does not guarantee protection to eggs on an individual basis, they may increase the probability that some eggs in a clutch are left intact thereby potentially conferring a fitness advantage to more offspring than if eggs are left unprotected. Based on HPLC analysis we found that maternal contribution of cardenolides was significantly greater than paternal contribution of cardenolides to the eggs, supporting the results of our predation trials that a maternal diet of Milkweed makes eggs more distasteful than a paternal diet of Milkweed.
Adam Bewick - One of the best experts on this subject based on the ideXlab platform.
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Dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug, Oncopeltus fasciatus
Epigenetics & Chromatin, 2019Co-Authors: Adam Bewick, Zachary Sanchez, Allen J Moore, Elizabeth C Mckinney, Patricia J Moore, Robert J SchmitzAbstract: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 .
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dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug oncopeltus fasciatus
Epigenetics & Chromatin, 2019Co-Authors: Adam Bewick, Zachary Sanchez, Allen J Moore, Elizabeth C Mckinney, Patricia J Moore, Robert J SchmitzAbstract:The function of cytosine (DNA) methylation in insects remains inconclusive due to a lack of mutant and/or genetic studies. 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. 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.
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MOESM1 of Dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug, Oncopeltus fasciatus
2019Co-Authors: Adam Bewick, Zachary Sanchez, Elizabeth Mckinney, Allen Moore, Patricia Moore, Robert SchmitzAbstract:Additional file 1: Fig. S1. Identification of O. fasciatus DNA methyltransferases. a Phylogenetic relationship of DNA methyltransferases identified the de novo (Dnmt3) and maintenance (Dnmt1) DNA methyltransferase in O. fasciatus. Node support with ≤ 0.5 posterior probability is indicated—other nodes are ≥ 0.95. Branch lengths are in amino acid substitutions per site. Species names are represented as abbreviations: Acy. pis.: Acyrthosiphon pisum, Aed. aeg.: Aedes aegypti, Aed. alb.: Aedes albopictus, Ano. gam.: Anopheles gambiae, Api. mel.: A. mellifera, Bom. mor.: Bo. mori, Cam. flo.: Camponotus floridanus, Cop. flo.: Copidosoma floridanum, Cul. qui.: Culex pipiens quinquefasciatus, Dro. mel.: Drosophila melanogaster, Har. sal.: Harpegnathos saltator, Mic. dem.: Microplitis demolitor, Nas. vit.: Nasonia vitripennis, Nic. ves.: Nicrophorus vespilloides, Onc. fas.: O. fasciatus, Cer. bir.: Ooceraea (Cerapachys) biroi, Pol. can.: Polistes canadensis, Pol. dom.: Polistes dominula, Sol. inv.: Solenopsis invicta, Tri. cas.: Tribolium castaneum, and Zoo. nev.: Z. nevadensis. b A to scale representation of Dnmt1 and protein domains identified in O. fasciatus and M. musculus. Fig. S2. Assessment of RNAi treatment targeting S-adenosyl-L-methionine (AdoMet) region (ds-dnmt1-2) of Dnmt1 produces similar results as ds-dnmt1-1. a Assessment of RNAi treatment targeting Dnmt1 using qRT-PCR demonstrates successful reduction in transcription in ovaries compared to control. b Whole ovaries from ds-dnmt1-2 females removed 12–14 days post-injection. c Control follicular epithelium nuclei. d ds-dnmt1-1 follicular epithelium nuclei. e ds-dnmt1-2 follicular epithelium nuclei. For c–e scale bar corresponds to 100 µm. Fig. S3. DNA methylation consequences following posttranscriptional knockdown of Dnmt1 are restricted to ovaries. a Assessment of RNAi treatment targeting Dnmt1 using qRT-PCR demonstrates successful reduction in transcription compared to control across all tissues sampled. Colored dots indicate independent biological replicates. b Genome-wide CG methylation level across tissues sampled. Numbers at the top of each bar correspond to a unique individual identifier. Fig. S4. Eggs laid in O. fasciatus ds-dnmt1-1 and control females. Number of eggs laid by ds-dnmt1-1 and control females 8 days post-injection. Dots indicate mean expression level, and error bars indicate standard error of the mean. Fig. S5. Expression of Dnmt3 is not affected by dsRNA targeting Dnmt1 (ds-dnmt1-1). Dots indicate mean expression level, and error bars indicate standard error of the mean. Fig. S6. mCG in A. mellifera and Z. nevadensis is not associated with transcription. a Gene expression level for deciles of increasing mCG (1–10) and unmethylated genes (UM). Error bars represent 95% confidence interval of the mean. b Regression of gene expression against a continuous measure of mCG among all genes with > 0 FPKM and weighted mCG. Raw p values are provided for each regression, and significance (S) or non-significance (NS) is indicated in brackets following Bonferroni correction. c. The relationship between change in gene expression measured as the log2 fold-change of FPKM between A. mellifera dnmt3 knockdown and GFP control, and DNA methylation measured as the difference between A. mellifera dnmt3 knockdown and GFP control mCG levels. For gene expression, FPKM values were averaged across libraries. Density of bins corresponds to the number of genes with similar changes to expression and DNA methylation. Fig. S7. Expression changes of differentially methylated genes. A heatmap showing gene expression changes for genes that are differentially CG-methylated between O. fasciatus ds-dnmt1-1 and control. Expression was standardized by the highest value per gene per biological replicate to produce a relative fragments per kilobase of transcript per million (RFPKM) value. RFPKM were clustered using a hierarchical clustering method. Fig. S8. Loss of mCG in O. fasciatus ovaries has a limited effect on transcription. Combinational overlap of genes that are differential CG-methylated and expressed, and similarly CG-methylated and expressed between O. fasciatus ds-dnmt1-1 and control. Gene groups: differentially methylated gene (DMG), differentially expressed gene (DEG), similarly methylated gene (SMG)/unmethylated genes (UMG), and non-differentially expressed gene (non-DEG). More stringent thresholds were used to group genes as CG-methylated or unmethylated (see “Materials and methods”). Fig. S9. DNA methylation of TEs in O. fasciatus. Levels of mCG across the bodies and 1 kb flanking sequence of different annotated TEs in O. fasciatus. Table S1. PCR primers used to validate the presence of a single Dnmt1 ortholog in the O. fasciatus genome. Table S2. Primer sequences for use in producing template DNA for use in the MegaScript transcription kit to generate double-stranded RNAs for injection and for quantitative real-time PCR to assess expression levels of Dnmt1. Table S3. DNA methylation summary statistics for all species investigated in this study. Table S4. Output from edgeR v3.20.1 [69] with gene expression (fragments per kilobase of transcript per million mapped reads [FPKM]) for O. fasciatus ovaries ds-dnmt1-1 and control biological and technical replicates. Table S5. Gene expression (FPKM) for A. mellifera queen and drone brains. Table S6. Gene expression (FPKM) for A. mellifera dnmt3 knockdown and GFP control. Table S7. Gene expression (FPKM) for Z. nevadensis female worker at the final instar larva. Table S8. Output from edgeR v3.20.1 [69] with gene expression (FPKM) for O. fasciatus gut, head, and thorax ds-dnmt1-1 and control biological replicates. Table S9. Overlap between O. fasciatus (control) CG-methylated and unmethylated genes in none and ≥ 1 other insect species used in this study. Table S10. Output General Features File (GFF) from RepeatMasker v4.0.5 ( http://www.repeatmasker.org ). Table S11. Significance (p value) of TE expression between ds-dnmt1-1 and control tissues. Table S12. Gene Ontology (GO) terms for O. fasciatus v1.1 reference genome assembly [32] annotated genes. Table S13. Significantly enriched GO terms for the intersections between differentially methylated genes (DMG), similarly methylated genes (SMG), differentially expressed genes (DEG), and non-differentially expressed genes (non-DEG). Data S1. Unaligned and aligned DNA methyltransferase protein sequences in FASTA format, and a parenthetical phylogenetic tree in nexus format estimated from the aligned DNA methyltransferase protein sequences using BEAST v2.3.2 [51]
Zachary Sanchez - One of the best experts on this subject based on the ideXlab platform.
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Dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug, Oncopeltus fasciatus
Epigenetics & Chromatin, 2019Co-Authors: Adam Bewick, Zachary Sanchez, Allen J Moore, Elizabeth C Mckinney, Patricia J Moore, Robert J SchmitzAbstract: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 .
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dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug oncopeltus fasciatus
Epigenetics & Chromatin, 2019Co-Authors: Adam Bewick, Zachary Sanchez, Allen J Moore, Elizabeth C Mckinney, Patricia J Moore, Robert J SchmitzAbstract:The function of cytosine (DNA) methylation in insects remains inconclusive due to a lack of mutant and/or genetic studies. 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. 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.
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MOESM1 of Dnmt1 is essential for egg production and embryo viability in the Large Milkweed Bug, Oncopeltus fasciatus
2019Co-Authors: Adam Bewick, Zachary Sanchez, Elizabeth Mckinney, Allen Moore, Patricia Moore, Robert SchmitzAbstract:Additional file 1: Fig. S1. Identification of O. fasciatus DNA methyltransferases. a Phylogenetic relationship of DNA methyltransferases identified the de novo (Dnmt3) and maintenance (Dnmt1) DNA methyltransferase in O. fasciatus. Node support with ≤ 0.5 posterior probability is indicated—other nodes are ≥ 0.95. Branch lengths are in amino acid substitutions per site. Species names are represented as abbreviations: Acy. pis.: Acyrthosiphon pisum, Aed. aeg.: Aedes aegypti, Aed. alb.: Aedes albopictus, Ano. gam.: Anopheles gambiae, Api. mel.: A. mellifera, Bom. mor.: Bo. mori, Cam. flo.: Camponotus floridanus, Cop. flo.: Copidosoma floridanum, Cul. qui.: Culex pipiens quinquefasciatus, Dro. mel.: Drosophila melanogaster, Har. sal.: Harpegnathos saltator, Mic. dem.: Microplitis demolitor, Nas. vit.: Nasonia vitripennis, Nic. ves.: Nicrophorus vespilloides, Onc. fas.: O. fasciatus, Cer. bir.: Ooceraea (Cerapachys) biroi, Pol. can.: Polistes canadensis, Pol. dom.: Polistes dominula, Sol. inv.: Solenopsis invicta, Tri. cas.: Tribolium castaneum, and Zoo. nev.: Z. nevadensis. b A to scale representation of Dnmt1 and protein domains identified in O. fasciatus and M. musculus. Fig. S2. Assessment of RNAi treatment targeting S-adenosyl-L-methionine (AdoMet) region (ds-dnmt1-2) of Dnmt1 produces similar results as ds-dnmt1-1. a Assessment of RNAi treatment targeting Dnmt1 using qRT-PCR demonstrates successful reduction in transcription in ovaries compared to control. b Whole ovaries from ds-dnmt1-2 females removed 12–14 days post-injection. c Control follicular epithelium nuclei. d ds-dnmt1-1 follicular epithelium nuclei. e ds-dnmt1-2 follicular epithelium nuclei. For c–e scale bar corresponds to 100 µm. Fig. S3. DNA methylation consequences following posttranscriptional knockdown of Dnmt1 are restricted to ovaries. a Assessment of RNAi treatment targeting Dnmt1 using qRT-PCR demonstrates successful reduction in transcription compared to control across all tissues sampled. Colored dots indicate independent biological replicates. b Genome-wide CG methylation level across tissues sampled. Numbers at the top of each bar correspond to a unique individual identifier. Fig. S4. Eggs laid in O. fasciatus ds-dnmt1-1 and control females. Number of eggs laid by ds-dnmt1-1 and control females 8 days post-injection. Dots indicate mean expression level, and error bars indicate standard error of the mean. Fig. S5. Expression of Dnmt3 is not affected by dsRNA targeting Dnmt1 (ds-dnmt1-1). Dots indicate mean expression level, and error bars indicate standard error of the mean. Fig. S6. mCG in A. mellifera and Z. nevadensis is not associated with transcription. a Gene expression level for deciles of increasing mCG (1–10) and unmethylated genes (UM). Error bars represent 95% confidence interval of the mean. b Regression of gene expression against a continuous measure of mCG among all genes with > 0 FPKM and weighted mCG. Raw p values are provided for each regression, and significance (S) or non-significance (NS) is indicated in brackets following Bonferroni correction. c. The relationship between change in gene expression measured as the log2 fold-change of FPKM between A. mellifera dnmt3 knockdown and GFP control, and DNA methylation measured as the difference between A. mellifera dnmt3 knockdown and GFP control mCG levels. For gene expression, FPKM values were averaged across libraries. Density of bins corresponds to the number of genes with similar changes to expression and DNA methylation. Fig. S7. Expression changes of differentially methylated genes. A heatmap showing gene expression changes for genes that are differentially CG-methylated between O. fasciatus ds-dnmt1-1 and control. Expression was standardized by the highest value per gene per biological replicate to produce a relative fragments per kilobase of transcript per million (RFPKM) value. RFPKM were clustered using a hierarchical clustering method. Fig. S8. Loss of mCG in O. fasciatus ovaries has a limited effect on transcription. Combinational overlap of genes that are differential CG-methylated and expressed, and similarly CG-methylated and expressed between O. fasciatus ds-dnmt1-1 and control. Gene groups: differentially methylated gene (DMG), differentially expressed gene (DEG), similarly methylated gene (SMG)/unmethylated genes (UMG), and non-differentially expressed gene (non-DEG). More stringent thresholds were used to group genes as CG-methylated or unmethylated (see “Materials and methods”). Fig. S9. DNA methylation of TEs in O. fasciatus. Levels of mCG across the bodies and 1 kb flanking sequence of different annotated TEs in O. fasciatus. Table S1. PCR primers used to validate the presence of a single Dnmt1 ortholog in the O. fasciatus genome. Table S2. Primer sequences for use in producing template DNA for use in the MegaScript transcription kit to generate double-stranded RNAs for injection and for quantitative real-time PCR to assess expression levels of Dnmt1. Table S3. DNA methylation summary statistics for all species investigated in this study. Table S4. Output from edgeR v3.20.1 [69] with gene expression (fragments per kilobase of transcript per million mapped reads [FPKM]) for O. fasciatus ovaries ds-dnmt1-1 and control biological and technical replicates. Table S5. Gene expression (FPKM) for A. mellifera queen and drone brains. Table S6. Gene expression (FPKM) for A. mellifera dnmt3 knockdown and GFP control. Table S7. Gene expression (FPKM) for Z. nevadensis female worker at the final instar larva. Table S8. Output from edgeR v3.20.1 [69] with gene expression (FPKM) for O. fasciatus gut, head, and thorax ds-dnmt1-1 and control biological replicates. Table S9. Overlap between O. fasciatus (control) CG-methylated and unmethylated genes in none and ≥ 1 other insect species used in this study. Table S10. Output General Features File (GFF) from RepeatMasker v4.0.5 ( http://www.repeatmasker.org ). Table S11. Significance (p value) of TE expression between ds-dnmt1-1 and control tissues. Table S12. Gene Ontology (GO) terms for O. fasciatus v1.1 reference genome assembly [32] annotated genes. Table S13. Significantly enriched GO terms for the intersections between differentially methylated genes (DMG), similarly methylated genes (SMG), differentially expressed genes (DEG), and non-differentially expressed genes (non-DEG). Data S1. Unaligned and aligned DNA methyltransferase protein sequences in FASTA format, and a parenthetical phylogenetic tree in nexus format estimated from the aligned DNA methyltransferase protein sequences using BEAST v2.3.2 [51]
Moore, Allen J. - One of the best experts on this subject based on the ideXlab platform.
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Data from: Maternal effects and maternal selection arising from variation in allocation of free amino acid to eggs
2015Co-Authors: Newcombe Devi, Hunt John, Mitchell Christopher, Moore, Allen J.Abstract:Maternal provisioning can have profound effects on offspring phenotypes, or maternal effects, especially early in life. One ubiquitous form of provisioning is in the makeup of egg. However, only a few studies examine the role of specific egg constituents in maternal effects, especially as they relate to maternal selection (a standardized selection gradient reflecting the covariance between maternal traits and offspring fitness). Here, we report on the evolutionary consequences of differences in maternal acquisition and allocation of amino acids to eggs. We manipulated acquisition by varying maternal diet (Milkweed or sunflower) in the Large Milkweed Bug, Oncopeltus fasciatus. Variation in allocation was detected by examining two source populations with different evolutionary histories and life-history response to sunflower as food. We measured amino acids composition in eggs in this 2 × 2 design and found significant effects of source population and maternal diet on egg and nymph mass and of source population, maternal diet, and their interaction on amino acid composition of eggs. We measured significant linear and quadratic maternal selection on offspring mass associated with variation in amino acid allocation. Visualizing the performance surface along the major axes of nonlinear selection and plotting the mean amino acid profile of eggs from each treatment onto the surface revealed a saddle-shaped fitness surface. While maternal selection appears to have influenced how females allocate amino acids, this maternal effect did not evolve equally in the two populations. Furthermore, none of the population means coincided with peak performance. Thus, we found that the composition of free amino acids in eggs was due to variation in both acquisition and allocation, which had significant fitness effects and created selection. However, although there can be an evolutionary response to novel food resources, females may be constrained from reaching phenotypic optima with regard to allocation of free amino acids
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Maternal effects and maternal selection arising from variation in allocation of free amino acid to eggs
'Wiley', 2015Co-Authors: Newcombe Devi, Hunt, John E., Mitchell, Christopher A., Moore, Allen J.Abstract:Maternal provisioning can have profound effects on offspring phenotypes, or maternal effects, especially early in life. One ubiquitous form of provisioning is in the makeup of egg. However, only a few studies examine the role of specific egg constituents in maternal effects, especially as they relate to maternal selection (a standardized selection gradient reflecting the covariance between maternal traits and offspring fitness). Here, we report on the evolutionary consequences of differences in maternal acquisition and allocation of amino acids to eggs. We manipulated acquisition by varying maternal diet (Milkweed or sunflower) in the Large Milkweed Bug, Oncopeltus fasciatus. Variation in allocation was detected by examining two source populations with different evolutionary histories and life-history response to sunflower as food. We measured amino acids composition in eggs in this 2 × 2 design and found significant effects of source population and maternal diet on egg and nymph mass and of source population, maternal diet, and their interaction on amino acid composition of eggs. We measured significant linear and quadratic maternal selection on offspring mass associated with variation in amino acid allocation. Visualizing the performance surface along the major axes of nonlinear selection and plotting the mean amino acid profile of eggs from each treatment onto the surface revealed a saddle-shaped fitness surface. While maternal selection appears to have influenced how females allocate amino acids, this maternal effect did not evolve equally in the two populations. Furthermore, none of the population means coincided with peak performance. Thus, we found that the composition of free amino acids in eggs was due to variation in both acquisition and allocation, which had significant fitness effects and created selection. However, although there can be an evolutionary response to novel food resources, females may be constrained from reaching phenotypic optima with regard to allocation of free amino acids
