Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [ATAC-seq]
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ABSTRACT:
PROVIDER: PRJNA493085 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7901037_1.fastq.gz | Fastqsanger.gz | |||
| SRR7901037_2.fastq.gz | Fastqsanger.gz | |||
| SRR7901038_1.fastq.gz | Fastqsanger.gz | |||
| SRR7901038_2.fastq.gz | Fastqsanger.gz | |||
| SRR7901039_1.fastq.gz | Fastqsanger.gz |
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Project description:The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. Here we show that the recently published P. virginalis draft genome sequence encodes a conserved DNA methylation system. Whole-genome bisulfite sequencing of multiple replicates and different tissues revealed a methylation pattern that is characterized by gene body methylation of housekeeping genes. Interestingly, this pattern was largely tissue-invariant, suggesting a function that is unrelated to cell-fate specification. Indeed, integrative analysis of RNA-seq datasets showed that gene body methylation correlated with stable gene expression, while unmethylated genes often showed a high degree of inter-individual expression variation. Our findings thus establish the methylome of an emerging model organism and suggest that methylation-dependent regulation of gene expression variability may facilitate the phenotypic adaptation and invasive spread of this animal.
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Project description:The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. Here we show that the recently published P. virginalis draft genome sequence encodes a conserved DNA methylation system. Whole-genome bisulfite sequencing of multiple replicates and different tissues revealed a methylation pattern that is characterized by gene body methylation of housekeeping genes. Interestingly, this pattern was largely tissue-invariant, suggesting a function that is unrelated to cell-fate specification. Indeed, integrative analysis of RNA-seq datasets showed that gene body methylation correlated with stable gene expression, while unmethylated genes often showed a high degree of inter-individual expression variation. Our findings thus establish the methylome of an emerging model organism and suggest that methylation-dependent regulation of gene expression variability may facilitate the phenotypic adaptation and invasive spread of this animal.
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Project description:The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. Here we show that the recently published P. virginalis draft genome sequence encodes a conserved DNA methylation system. Whole-genome bisulfite sequencing of multiple replicates and different tissues revealed a methylation pattern that is characterized by gene body methylation of housekeeping genes. Interestingly, this pattern was largely tissue-invariant, suggesting a function that is unrelated to cell-fate specification. Indeed, integrative analysis of RNA-seq datasets showed that gene body methylation correlated with stable gene expression, while unmethylated genes often showed a high degree of inter-individual expression variation. Our findings thus establish the methylome of an emerging model organism and suggest that methylation-dependent regulation of gene expression variability may facilitate the phenotypic adaptation and invasive spread of this animal.
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Project description:Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish
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Project description:Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [RNA-seq]
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Project description:Marbled crayfish (Procambarus virginalis) are a parthenogenetically reproducing, globally invasive freshwater crayfish species. Previous work has shown that the global population is characterized by a monoclonal genome, which raises important questions about the mechanisms that promote their invasiveness. Dnmt1 is an evolutionarily conserved DNA methyltransferase responsible for maintaining 5-methylcytosine (5mC) patterns across the genome. While its relevance in transcriptional regulation and cell fate specification is well established, its role in ecological adaptation remains poorly understood. Here we show that environmental changes lead to significant downregulation of Dnmt1 in marbled crayfish. When mimicking this effect through a dsRNA-based in vivo knockdown of Dnmt1, we observed that invasiveness-related behavioral traits, such as activity and boldness were enhanced. Using image cytometry and single-cell RNA sequencing, we also detected an increase in the most mature immune cell type, the granular cells and depletion of hemocyte-derived neuronal precursors, which support adult neurogenesis. Further analysis by whole-genome bisulfite sequencing showed that these phenotypic changes are underpinned by a global reduction in gene body DNA methylation and a dysregulation of genes involved in nervous and immune system functions. Additionally, we observed nucleosome destabilization as a key mechanism influencing transcriptional changes after methylation loss. Our findings highlight a role for Dnmt1 in the canalization of cellular and organismal phenotypes, and provide a paradigm for how downregulation of Dnmt1 can enhance invasive traits.
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Project description:Marbled crayfish (Procambarus virginalis) are a parthenogenetically reproducing, globally invasive freshwater crayfish species. Previous work has shown that the global population is characterized by a monoclonal genome, which raises important questions about the mechanisms that promote their invasiveness. Dnmt1 is an evolutionarily conserved DNA methyltransferase responsible for maintaining 5-methylcytosine (5mC) patterns across the genome. While its relevance in transcriptional regulation and cell fate specification is well established, its role in ecological adaptation remains poorly understood. Here we show that environmental changes lead to significant downregulation of Dnmt1 in marbled crayfish. When mimicking this effect through a dsRNA-based in vivo knockdown of Dnmt1, we observed that invasiveness-related behavioral traits, such as activity and boldness were enhanced. Using image cytometry and single-cell RNA sequencing, we also detected an increase in the most mature immune cell type, the granular cells and depletion of hemocyte-derived neuronal precursors, which support adult neurogenesis. Further analysis by whole-genome bisulfite sequencing showed that these phenotypic changes are underpinned by a global reduction in gene body DNA methylation and a dysregulation of genes involved in nervous and immune system functions. Additionally, we observed nucleosome destabilization as a key mechanism influencing transcriptional changes after methylation loss. Our findings highlight a role for Dnmt1 in the canalization of cellular and organismal phenotypes, and provide a paradigm for how downregulation of Dnmt1 can enhance invasive traits.
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