Ontology highlight
ABSTRACT:
PROVIDER: PRJEB53983 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
2018-10-11 | GSE120450 | GEO
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.
2018-10-11 | GSE120358 | GEO
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.
2018-10-11 | GSE112410 | GEO
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.
2018-10-11 | GSE112409 | GEO
Project description:DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.
2023-03-02 | GSE210293 | GEO
Project description:DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.
2023-03-02 | GSE210211 | GEO
Project description:DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.
2023-03-02 | GSE210210 | GEO
Project description:DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.
2023-03-02 | GSE210208 | GEO
Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes. A customized bovine Combimatrix microarray containing 10,199 genes were constructed, and transcripome of longissimus dorsi muscle was compared between Korean cattle bulls (3 bulls) and steers (3 high-marbled and 3 low-marbled steers) by using the microarray hybridzation.
2013-06-30 | E-GEOD-35085 | biostudies-arrayexpress