RNA interference knockdown of
            <i>DNA methyl-transferase 3</i>
            affects gene alternative splicing in the honey bee

Li-Byarlay, Hongmei; Li, Yang; Stroud, Hume; Feng, Suhua; Newman, Thomas C.; Kaneda, Megan M.; Hou, Kirk K.; Worley, Kim C.; Elsik, Christine G.; Wickline, Samuel A.; Jacobsen, Steven E.; Ma, Jian; Robinson, Gene E.

doi:10.1073/pnas.1310735110

Cited by 225 publications

(247 citation statements)

References 41 publications

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“…Regardless, the association between alternative splicing and DNA methylation we observed in this termite (Fig. 6c) supports the hypothesis that intragenic DNA methylation interacts with messenger RNA splicing to produce an array of phenotypes in eusocial insects 67,69 . Collectively, the results of our genome analyses substantially improve our understanding of the mechanisms that have allowed termites to develop and maintain a high degree of social complexity, providing a much needed comparative counterpoint to the wealth of genomic information available for eusocial Hymenoptera.…”

Section: Discussionsupporting

confidence: 82%

Molecular traces of alternative social organization in a termite genome

et al. 2014

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Although eusociality evolved independently within several orders of insects, research into the molecular underpinnings of the transition towards social complexity has been confined primarily to Hymenoptera (for example, ants and bees). Here we sequence the genome and stage-specific transcriptomes of the dampwood termite Zootermopsis nevadensis (Blattodea) and compare them with similar data for eusocial Hymenoptera, to better identify commonalities and differences in achieving this significant transition. We show an expansion of genes related to male fertility, with upregulated gene expression in male reproductive individuals reflecting the profound differences in mating biology relative to the Hymenoptera. For several chemoreceptor families, we show divergent numbers of genes, which may correspond to the more claustral lifestyle of these termites. We also show similarities in the number and expression of genes related to caste determination mechanisms. Finally, patterns of DNA methylation and alternative splicing support a hypothesized epigenetic regulation of caste differentiation.

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Section: Discussionsupporting

confidence: 82%

Molecular traces of alternative social organization in a termite genome

et al. 2014

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“…3E). This result may limit the role of DNA methylation in regulating phenotype-associated gene expression or alternative splicing in our species, and contrasts with what has been described in the honey bee (26,(35)(36)(37)(38)(39).…”

Section: No Distinct Methylation Patterning Across the Genome Or Betweencontrasting

confidence: 80%

“…In both P. canadensis and D. quadriceps, DNA methylation is dispersed sparsely across genes (Fig. 3C), particularly in P. canadensis, whose genome lacks a DNA methyltransferase 3 (DNMT3) gene, an enzyme involved in de novo methylation (25,26) (Fig. S4A and S5A and SI Text, section IV.5).…”

Section: No Distinct Methylation Patterning Across the Genome Or Betweenmentioning

confidence: 99%

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

Patalano

Vlasova

Wyatt

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.

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“…24). Support for a role of DNA methylation in differential gene expression of social insects includes pharmacological disruptions of DNA methylation and RNA interference knockdowns of DNA methyltransferases that alter gene expression (48). However, it could be argued that these effects might represent by-products of genome-wide disruption in DNA methylation, rather than a specific targeted role of methylation in development and differentiation by sex or caste.…”

Section: Resultsmentioning

confidence: 99%

Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

Wang

Werren

Clark

2015

Proc. Natl. Acad. Sci. U.S.A.

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There is extraordinary diversity in sexual dimorphism (SD) among animals, but little is known about its epigenetic basis. To study the epigenetic architecture of SD in a haplodiploid system, we performed RNA-seq and whole-genome bisulfite sequencing of adult females and males from two closely related parasitoid wasps, Nasonia vitripennis and Nasonia giraulti. More than 75% of expressed genes displayed significantly sex-biased expression. As a consequence, expression profiles are more similar between species within each sex than between sexes within each species. Furthermore, extremely male-and female-biased genes are enriched for totally different functional categories: male-biased genes for key enzymes in sexpheromone synthesis and female-biased genes for genes involved in epigenetic regulation of gene expression. Remarkably, just 70 highly expressed, extremely male-biased genes account for 10% of all transcripts in adult males. Unlike expression profiles, DNA methylomes are highly similar between sexes within species, with no consistent sex differences in methylation found. Therefore, methylation changes cannot explain the extensive level of sex-biased gene expression observed. Female-biased genes have smaller sequence divergence between species, higher conservation to other hymenopterans, and a broader expression range across development. Overall, female-biased genes have been recruited from genes with more conserved and broadly expressing "house-keeping" functions, whereas male-biased genes are more recently evolved and are predominately testis specific. In summary, Nasonia accomplish a striking degree of sex-biased expression without sex chromosomes or epigenetic differences in methylation. We propose that methylation provides a general signal for constitutive gene expression, whereas other sex-specific signals cause sex-biased gene expression.sex-biased expression | DNA methylation | RNA-seq | WGBS-seq | fatty acid desaturase

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RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee

Cited by 225 publications

References 41 publications

Molecular traces of alternative social organization in a termite genome

Molecular traces of alternative social organization in a termite genome

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

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