The DNA methyltransferase family: a versatile toolkit for epigenetic regulation

Nature Reviews Genetics, Год журнала: 2017, Номер 19(2), С. 81 - 92

Опубликована: Окт. 16, 2017

Язык: Английский

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The locust genome provides insight into swarm formation and long-distance flight

Nature Communications, Год журнала: 2014, Номер 5(1)

Опубликована: Янв. 14, 2014

Locusts are one of the world's most destructive agricultural pests and represent a useful model system in entomology. Here we present draft 6.5 Gb genome sequence Locusta migratoria, which is largest animal sequenced so far. Our findings indicate that large size L. migratoria likely to be because transposable element proliferation combined with slow rates loss for these elements. Methylome transcriptome analyses reveal complex regulatory mechanisms involved microtubule dynamic-mediated synapse plasticity during phase change. We find significant expansion gene families associated energy consumption detoxification, consistent long-distance flight capacity phytophagy. report hundreds potential insecticide target genes, including cys-loop ligand-gated ion channels, G-protein-coupled receptors lethal genes. The offers new insights into biology sustainable management this pest species, will promote its wide use as system. serve organism studies insects. Here, authors migratory locust, provide insight genes key survival traits such phase-change, migration feeding.

Язык: Английский

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Epigenetic modification and inheritance in sexual reversal of fish

Genome Research, Год журнала: 2014, Номер 24(4), С. 604 - 615

Опубликована: Фев. 2, 2014

Environmental sex determination (ESD) occurs in divergent, phylogenetically unrelated taxa, and some species, co-occurs with genetic (GSD) mechanisms. Although epigenetic regulation response to environmental effects has long been proposed be associated ESD, a systemic analysis on of ESD is still lacking. Using half-smooth tongue sole ( Cynoglossus semilaevis ) as model—a marine fish that both ZW chromosomal GSD temperature-dependent ESD—we investigated the role DNA methylation transition from ESD. Comparative gonadal methylomes pseudomale, female, normal male revealed genes pathways are major targets substantial modification during sexual reversal. Methylation pseudomales globally inherited their offspring, which can naturally develop into without temperature incubation. Transcriptome dosage compensation restricted, methylated cytosine enriched Z region pseudomale testes, achieving equal expression level testes. In contrast, female-specific W suppressed by regulation. We conclude plays multiple crucial roles reversal fish. also offer first clues mechanisms behind gene balancing an organism undergoes Finally, we suggest causal link between bias chromosome assortment offspring family transgenerational inheritance

Язык: Английский

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Evolution of DNA Methylation across Insects

Molecular Biology and Evolution, Год журнала: 2016, Номер unknown, С. msw264 - msw264

Опубликована: Ноя. 19, 2016

DNA methylation contributes to gene and transcriptional regulation in eukaryotes, therefore has been hypothesized facilitate the evolution of plastic traits such as sociality insects. However, is sparsely studied Therefore, we documented patterns across a wide diversity We predicted that underlying enzymatic machinery concordant with methylation. Finally, given suggestion facilitated social Hymenoptera, tested hypothesis system will be associated presence/absence among other insect orders. found widespread, detected all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed differed levels Hymenopteran (ants, bees, wasps sawflies) had some lowest levels, including several potential losses. Blattodea (cockroaches termites) show possible patterns, loss eusocial species whereas solitary highest levels. Species do not always possess typical machinery. identified duplication event maintenance methyltransferase 1 (DNMT1) shared by paralogs have experienced divergent, nonneutral evolution. This suggests alternative pathways may exist. Phylogenetically corrected comparisons revealed no evidence supports evolutionary association between Future functional studies required advance our understanding

Язык: Английский

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Alternative splicing as a source of phenotypic diversity

Nature Reviews Genetics, Год журнала: 2022, Номер 23(11), С. 697 - 710

Опубликована: Июль 12, 2022

Язык: Английский

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Epigenetics, plasticity, and evolution: How do we link epigenetic change to phenotype?

Journal of Experimental Zoology Part B Molecular and Developmental Evolution, Год журнала: 2014, Номер 322(4), С. 208 - 220

Опубликована: Апрель 9, 2014

Epigenetic mechanisms are proposed as an important way in which the genome responds to environment. marks, including DNA methylation and Histone modifications, can be triggered by environmental effects, lead permanent changes gene expression, affecting phenotype of organism. have been key plasticity, allowing exposure shape future expression. While we beginning understand how these roles human biology disease, little understanding their impacts on ecology evolution. In this review, discuss different types epigenetic expression methods for assaying changes, point out advances require fully impact field.

Язык: Английский

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Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Genome biology, Год журнала: 2018, Номер 19(1)

Опубликована: Март 15, 2018

Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, systematic evaluation biases WGBS strategies missing. We perform comparative analysis several commonly pre- post-bisulfite library protocols their performance quality outputs. Our results show that per se main trigger pronounced amplification builds on these underlying artefacts. The majority standard yield significantly biased sequence output overestimate global methylation. Importantly, absolute relative methylation levels at specific genomic regions vary substantially between methods, with clear implications DNA studies. amplification-free least approach WGBS. In choice protocol or polymerase can minimize To aid assessment existing datasets, we have integrated bias diagnostic tool Bismark package offer approaches consideration during datasets.

Язык: Английский

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Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

Genome Research, Год журнала: 2013, Номер 23(8), С. 1235 - 1247

Опубликована: Май 1, 2013

Genomes of eusocial insects code for dramatic examples phenotypic plasticity and social organization. We compared the genomes seven ants, honeybee, various solitary to examine whether lineages share distinct features genomic Each ant lineage contains ∼4000 novel genes, but only 64 these genes are conserved among all ants. Many gene families have been expanded in notably those involved chemical communication (e.g., desaturases odorant receptors). Alignment revealed reduced purifying selection with Drosophila without significantly synteny. Correspondingly, exhibit divergence noncoding regulatory elements; however, extant regions enriched RNAs transcription factor-binding sites. Comparison orthologous promoters between species significant evolution both cis Creb) trans fork head) nearly 2000 many which plasticity. Our results emphasize that changes can occur remarkably fast because two recently diverged leaf-cutter faster accumulation species-specific greater elements other ants or Drosophila. Thus, while "socio-genomes" honeybee broadly characterized by a pervasive pattern composition regulation, they preserve lineage-specific linked eusociality. propose regulation played key role origins insect eusociality, whereas were more relevant adaptations.

Язык: Английский

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

Proceedings of the National Academy of Sciences, Год журнала: 2015, Номер 112(45), С. 13970 - 13975

Опубликована: Окт. 19, 2015

Significance In eusocial insect societies, such as ants and some bees wasps, phenotypes are highly plastic, generating alternative (queens workers) from the same genome. The greatest plasticity is found in simple which individuals can switch between adults. genomic, transcriptional, epigenetic underpinnings of largely unknown. contrast to complex societies honeybee, we find that lack distinct transcriptional differentiation coherently patterned DNA methylomes. Instead, defined by subtle network organization. These traits may facilitate genomic plasticity. insights resources will stimulate new approaches hypotheses help unravel processes create phenotypic

Язык: Английский

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

Proceedings of the National Academy of Sciences, Год журнала: 2013, Номер 110(31), С. 12750 - 12755

Опубликована: Июль 12, 2013

Studies of DNA methylation from fungi, plants, and animals indicate that gene body is ancient highly conserved in eukaryotic genomes, but its role has not been clearly defined. It postulated regulation alternative splicing transcripts was an original function methylation, a direct experimental test the effect on slicing at whole genome level never performed. To do this, we developed unique method to administer RNA interference (RNAi) high-throughput noninvasive manner then used it knock down expression methyl-transferase 3 ( dnmt3 ), which required for de novo methylation. We chose honey bee Apis mellifera ) this because recently emerged as important model organism studying effects development social behavior, bees predominantly bodies. Here show RNAi decreased global genomic expected addition caused widespread diverse changes fat tissue. Four different types events were affected by knockdown, change two types, exon skipping intron retention, directly related These results demonstrate one regulate splicing.

Язык: Английский

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