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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ftpubmed:oai:pubmedcentral.nih.gov:3840415 2023-05-15T15:58:44+02:00 Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc Gavery, Mackenzie R. Roberts, Steven B. 2013-11-21 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840415 http://www.ncbi.nlm.nih.gov/pubmed/24282674 https://doi.org/10.7717/peerj.215 en eng PeerJ Inc. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840415 http://www.ncbi.nlm.nih.gov/pubmed/24282674 http://dx.doi.org/10.7717/peerj.215 © 2013 Gavery and Roberts http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Aquaculture Fisheries and Fish Science Text 2013 ftpubmed https://doi.org/10.7717/peerj.215 2013-12-01T01:38:45Z 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. Text Crassostrea gigas Pacific oyster PubMed Central (PMC) Pacific PeerJ 1 e215 |
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Aquaculture Fisheries and Fish Science |
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Aquaculture Fisheries and Fish Science Gavery, Mackenzie R. Roberts, Steven B. Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc |
topic_facet |
Aquaculture Fisheries and Fish Science |
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. |
format |
Text |
author |
Gavery, Mackenzie R. Roberts, Steven B. |
author_facet |
Gavery, Mackenzie R. Roberts, Steven B. |
author_sort |
Gavery, Mackenzie R. |
title |
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_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_sort |
predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc |
publisher |
PeerJ Inc. |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840415 http://www.ncbi.nlm.nih.gov/pubmed/24282674 https://doi.org/10.7717/peerj.215 |
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Pacific |
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Pacific |
genre |
Crassostrea gigas Pacific oyster |
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Crassostrea gigas Pacific oyster |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840415 http://www.ncbi.nlm.nih.gov/pubmed/24282674 http://dx.doi.org/10.7717/peerj.215 |
op_rights |
© 2013 Gavery and Roberts http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
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CC-BY |
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https://doi.org/10.7717/peerj.215 |
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e215 |
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