Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii
DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from Pinctad...
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| Veröffentlicht in: | Marine biotechnology (New York, N.Y.) N.Y.), 2020-06, Vol.22 (3), p.380-390 |
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| creator | Zhang, Jiabin Luo, Shaojie Gu, Zefeng Deng, Yuewen Jiao, Yu |
| description | DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from
Pinctada fucata martensii
. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from
P. f. martensii
via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of
P. f. martensii
and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation. |
| doi_str_mv | 10.1007/s10126-020-09957-4 |
| format | Article |
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Pinctada fucata martensii
. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from
P. f. martensii
via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of
P. f. martensii
and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation.</description><identifier>ISSN: 1436-2228</identifier><identifier>EISSN: 1436-2236</identifier><identifier>DOI: 10.1007/s10126-020-09957-4</identifier><identifier>PMID: 32140888</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Amino acids ; Animal Shells - metabolism ; Animals ; Biomedical and Life Sciences ; Calcification, Physiologic - genetics ; CpG islands ; Deoxyribonucleic acid ; DNA ; DNA Methylation ; DNA methyltransferase ; Energy metabolism ; Engineering ; Epigenetics ; Exons ; Freshwater & Marine Ecology ; Gene expression ; Gene Expression Profiling ; Genes ; Genomes ; Genomics ; Identification ; Immunoprecipitation ; Levels ; Life Sciences ; Mantle ; Marine molluscs ; Metabolism ; Microbiology ; Mineralization ; Nucleic acids ; Nucleotide sequence ; Original Article ; Pearl oysters ; Phenotypic plasticity ; Pinctada - genetics ; Pinctada - metabolism ; Pinctada fucata martensii ; Protein metabolism ; Protein synthesis ; Protein turnover ; Proteins ; Regulatory mechanisms (biology) ; Ribonucleic acid ; RNA ; Sequence Analysis, RNA ; Zoology</subject><ispartof>Marine biotechnology (New York, N.Y.), 2020-06, Vol.22 (3), p.380-390</ispartof><rights>Springer Science+Business Media, LLC, part of Springer Nature 2020</rights><rights>Springer Science+Business Media, LLC, part of Springer Nature 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-78c2b8a4a75d1f09cb28e9388613a75707db178216e216ba1104b7c4e80756493</citedby><cites>FETCH-LOGICAL-c375t-78c2b8a4a75d1f09cb28e9388613a75707db178216e216ba1104b7c4e80756493</cites><orcidid>0000-0002-1795-5255</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10126-020-09957-4$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10126-020-09957-4$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32140888$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Jiabin</creatorcontrib><creatorcontrib>Luo, Shaojie</creatorcontrib><creatorcontrib>Gu, Zefeng</creatorcontrib><creatorcontrib>Deng, Yuewen</creatorcontrib><creatorcontrib>Jiao, Yu</creatorcontrib><title>Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii</title><title>Marine biotechnology (New York, N.Y.)</title><addtitle>Mar Biotechnol</addtitle><addtitle>Mar Biotechnol (NY)</addtitle><description>DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from
Pinctada fucata martensii
. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from
P. f. martensii
via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of
P. f. martensii
and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation.</description><subject>Amino acids</subject><subject>Animal Shells - metabolism</subject><subject>Animals</subject><subject>Biomedical and Life Sciences</subject><subject>Calcification, Physiologic - genetics</subject><subject>CpG islands</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA methyltransferase</subject><subject>Energy metabolism</subject><subject>Engineering</subject><subject>Epigenetics</subject><subject>Exons</subject><subject>Freshwater & Marine Ecology</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Identification</subject><subject>Immunoprecipitation</subject><subject>Levels</subject><subject>Life Sciences</subject><subject>Mantle</subject><subject>Marine molluscs</subject><subject>Metabolism</subject><subject>Microbiology</subject><subject>Mineralization</subject><subject>Nucleic acids</subject><subject>Nucleotide sequence</subject><subject>Original Article</subject><subject>Pearl oysters</subject><subject>Phenotypic plasticity</subject><subject>Pinctada - genetics</subject><subject>Pinctada - metabolism</subject><subject>Pinctada fucata martensii</subject><subject>Protein metabolism</subject><subject>Protein synthesis</subject><subject>Protein turnover</subject><subject>Proteins</subject><subject>Regulatory mechanisms (biology)</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Sequence Analysis, 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DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii</title><author>Zhang, Jiabin ; Luo, Shaojie ; Gu, Zefeng ; Deng, Yuewen ; Jiao, Yu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-78c2b8a4a75d1f09cb28e9388613a75707db178216e216ba1104b7c4e80756493</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Amino acids</topic><topic>Animal Shells - metabolism</topic><topic>Animals</topic><topic>Biomedical and Life Sciences</topic><topic>Calcification, Physiologic - genetics</topic><topic>CpG islands</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>DNA methyltransferase</topic><topic>Energy metabolism</topic><topic>Engineering</topic><topic>Epigenetics</topic><topic>Exons</topic><topic>Freshwater & Marine Ecology</topic><topic>Gene expression</topic><topic>Gene Expression 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Jiabin</au><au>Luo, Shaojie</au><au>Gu, Zefeng</au><au>Deng, Yuewen</au><au>Jiao, Yu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii</atitle><jtitle>Marine biotechnology (New York, N.Y.)</jtitle><stitle>Mar Biotechnol</stitle><addtitle>Mar Biotechnol (NY)</addtitle><date>2020-06-01</date><risdate>2020</risdate><volume>22</volume><issue>3</issue><spage>380</spage><epage>390</epage><pages>380-390</pages><issn>1436-2228</issn><eissn>1436-2236</eissn><abstract>DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from
Pinctada fucata martensii
. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from
P. f. martensii
via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of
P. f. martensii
and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>32140888</pmid><doi>10.1007/s10126-020-09957-4</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-1795-5255</orcidid></addata></record> |
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| source | MEDLINE; SpringerLink |
| subjects | Amino acids Animal Shells - metabolism Animals Biomedical and Life Sciences Calcification, Physiologic - genetics CpG islands Deoxyribonucleic acid DNA DNA Methylation DNA methyltransferase Energy metabolism Engineering Epigenetics Exons Freshwater & Marine Ecology Gene expression Gene Expression Profiling Genes Genomes Genomics Identification Immunoprecipitation Levels Life Sciences Mantle Marine molluscs Metabolism Microbiology Mineralization Nucleic acids Nucleotide sequence Original Article Pearl oysters Phenotypic plasticity Pinctada - genetics Pinctada - metabolism Pinctada fucata martensii Protein metabolism Protein synthesis Protein turnover Proteins Regulatory mechanisms (biology) Ribonucleic acid RNA Sequence Analysis, RNA Zoology |
| title | Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii |
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