Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc
Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studie...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2013-11-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/215.pdf |
| _version_ | 1827605985575829504 |
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| author | Mackenzie R. Gavery Steven B. Roberts |
| author_facet | Mackenzie R. Gavery Steven B. Roberts |
| author_sort | Mackenzie R. Gavery |
| collection | DOAJ |
| description | Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves. |
| first_indexed | 2024-03-09T06:31:35Z |
| format | Article |
| id | doaj.art-ecc3d743988d4f2ea879ab9aeb91e354 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:31:35Z |
| publishDate | 2013-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj.art-ecc3d743988d4f2ea879ab9aeb91e3542023-12-03T11:05:36ZengPeerJ Inc.PeerJ2167-83592013-11-011e21510.7717/peerj.215215Predominant intragenic methylation is associated with gene expression characteristics in a bivalve molluscMackenzie R. Gavery0Steven B. Roberts1School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USASchool of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USACharacterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.https://peerj.com/articles/215.pdfDNA methylationEpigeneticsBivalveMolluscGene regulationMethylome |
| spellingShingle | Mackenzie R. Gavery Steven B. Roberts Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc PeerJ DNA methylation Epigenetics Bivalve Mollusc Gene regulation Methylome |
| title | Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc |
| title_full | Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc |
| title_fullStr | Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc |
| title_full_unstemmed | Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc |
| title_short | Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc |
| title_sort | predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc |
| topic | DNA methylation Epigenetics Bivalve Mollusc Gene regulation Methylome |
| url | https://peerj.com/articles/215.pdf |
| work_keys_str_mv | AT mackenziergavery predominantintragenicmethylationisassociatedwithgeneexpressioncharacteristicsinabivalvemollusc AT stevenbroberts predominantintragenicmethylationisassociatedwithgeneexpressioncharacteristicsinabivalvemollusc |