{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1360285711791109888.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1186/s12867-017-0083-2"}},{"identifier":{"@type":"URI","@value":"http://link.springer.com/content/pdf/10.1186/s12867-017-0083-2.pdf"}},{"identifier":{"@type":"URI","@value":"http://link.springer.com/article/10.1186/s12867-017-0083-2/fulltext.html"}},{"identifier":{"@type":"PMID","@value":"28279161"}}],"resourceType":"学術雑誌論文(journal article)","dc:title":[{"@value":"Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles"}],"description":[{"notation":[{"@value":"It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP.Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans.MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research."}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1380285711791109647","@type":"Researcher","foaf:name":[{"@value":"Toshiki Aiba"}]},{"@id":"https://cir.nii.ac.jp/crid/1380285711791109763","@type":"Researcher","foaf:name":[{"@value":"Toshiyuki Saito"}]},{"@id":"https://cir.nii.ac.jp/crid/1380285711791109773","@type":"Researcher","foaf:name":[{"@value":"Akiko Hayashi"}]},{"@id":"https://cir.nii.ac.jp/crid/1380285711791109889","@type":"Researcher","foaf:name":[{"@value":"Shinji Sato"}]},{"@id":"https://cir.nii.ac.jp/crid/1380285711791109641","@type":"Researcher","foaf:name":[{"@value":"Harunobu Yunokawa"}]},{"@id":"https://cir.nii.ac.jp/crid/1380285711791109762","@type":"Researcher","foaf:name":[{"@value":"Toru Maruyama"}]},{"@id":"https://cir.nii.ac.jp/crid/1380285711791109764","@type":"Researcher","foaf:name":[{"@value":"Wataru Fujibuchi"}]},{"@id":"https://cir.nii.ac.jp/crid/1380285711791109632","@type":"Researcher","foaf:name":[{"@value":"Hisaka Kurita"}]},{"@id":"https://cir.nii.ac.jp/crid/1380285711791109640","@type":"Researcher","foaf:name":[{"@value":"Chiharu Tohyama"}]},{"@id":"https://cir.nii.ac.jp/crid/1030003658395239680","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"00274837"},{"@type":"NRID","@value":"1000000274837"},{"@type":"NRID","@value":"9000018311625"},{"@type":"NRID","@value":"9000253282546"},{"@type":"NRID","@value":"9000020961601"},{"@type":"NRID","@value":"9000253285984"},{"@type":"NRID","@value":"9000005629204"},{"@type":"NRID","@value":"9000003107981"},{"@type":"NRID","@value":"9000021003696"},{"@type":"NRID","@value":"9000253284275"},{"@type":"NRID","@value":"9000005382385"},{"@type":"NRID","@value":"9000413359526"},{"@type":"NRID","@value":"9000252808523"},{"@type":"NRID","@value":"9000396103192"},{"@type":"NRID","@value":"9000021003578"},{"@type":"NRID","@value":"9000018603589"},{"@type":"NRID","@value":"9000283732408"},{"@type":"NRID","@value":"9000413359489"},{"@type":"NRID","@value":"9000325835191"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/S_Ohsako"}],"foaf:name":[{"@value":"Seiichiroh Ohsako"}]}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"14712199"}],"prism:publicationName":[{"@value":"BMC Molecular Biology"}],"dc:publisher":[{"@value":"Springer Science and Business Media LLC"}],"prism:publicationDate":"2017-03-09","prism:volume":"18","prism:number":"1","prism:startingPage":"7"},"reviewed":"false","dcterms:accessRights":"http://purl.org/coar/access_right/c_abf2","dc:rights":["http://creativecommons.org/licenses/by/4.0/","http://creativecommons.org/licenses/by/4.0/"],"url":[{"@id":"http://link.springer.com/content/pdf/10.1186/s12867-017-0083-2.pdf"},{"@id":"http://link.springer.com/article/10.1186/s12867-017-0083-2/fulltext.html"}],"createdAt":"2017-03-09","modifiedAt":"2024-06-22","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=Male","dc:title":"Male"},{"@id":"https://cir.nii.ac.jp/all?q=Methodology%20Article","dc:title":"Methodology Article"},{"@id":"https://cir.nii.ac.jp/all?q=DNA","dc:title":"DNA"},{"@id":"https://cir.nii.ac.jp/all?q=DNA%20Methylation","dc:title":"DNA Methylation"},{"@id":"https://cir.nii.ac.jp/all?q=Mice,%20Inbred%20C57BL","dc:title":"Mice, Inbred C57BL"},{"@id":"https://cir.nii.ac.jp/all?q=Animals","dc:title":"Animals"},{"@id":"https://cir.nii.ac.jp/all?q=CpG%20Islands","dc:title":"CpG Islands"},{"@id":"https://cir.nii.ac.jp/all?q=Amplified%20Fragment%20Length%20Polymorphism%20Analysis","dc:title":"Amplified Fragment Length Polymorphism Analysis"},{"@id":"https://cir.nii.ac.jp/all?q=Molecular%20Biology","dc:title":"Molecular Biology"}],"project":[{"@id":"https://cir.nii.ac.jp/crid/1040282256803370496","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"15H02830"},{"@type":"JGN","@value":"JP15H02830"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-15H02830/"}],"notation":[{"@language":"ja","@value":"環境化学物質曝露レベルに着目したエピゲノム刻印探索のためのMSD-AFLP法応用"},{"@language":"en","@value":"Application of MSD-AFLP method to explore epigenetic imprints focusing on exposure levels of environmental chemicals"}]},{"@id":"https://cir.nii.ac.jp/crid/1040282256936382208","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"17H06396"},{"@type":"JGN","@value":"JP17H06396"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PLANNED-17H06396/"}],"notation":[{"@language":"ja","@value":"環境ストレスによる生体応答、エピゲノムとプロテオーム解析"},{"@language":"en","@value":"Biological Response to Environmental Stress: Epigenome/Proteome Analysis"}]},{"@id":"https://cir.nii.ac.jp/crid/1040282257289244672","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"26670327"},{"@type":"JGN","@value":"JP26670327"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-26670327/"}],"notation":[{"@language":"ja","@value":"男児外陰部異常症における化学物質曝露バイオマーカーとＤＮＡメチル化レベルの関連性"},{"@language":"en","@value":"Relationship between chemical exposure biomarkers and DNA methylation levels in the malformations of external reproductive system of young males"}]}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360283694399379968","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"DNA Methylation Profiles at Precancerous Stages Associated with Recurrence of Lung Adenocarcinoma"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292617911094912","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292617916207488","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292619136547200","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292619370571520","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing"}]},{"@id":"https://cir.nii.ac.jp/crid/1360565167558939776","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574093772221184","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Epigenetic transgenerational inheritance of altered stress responses"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574094751193088","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"AFLP: a new technique for DNA fingerprinting"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574095339235584","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"High dose bisphenol A impairs hippocampal neurogenesis in female mice across generations"}]},{"@id":"https://cir.nii.ac.jp/crid/1360580232419169280","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"The Lysophospholipase PNPLA7 Controls Hepatic Choline and Methionine Metabolism"}]},{"@id":"https://cir.nii.ac.jp/crid/1360848662418537216","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Genome-Wide DNA Methylation Analysis Reveals Phytoestrogen Modification of Promoter Methylation Patterns during Embryonic Stem Cell Differentiation"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137043506717824","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"High density DNA methylation array with single CpG site resolution"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137045093902592","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Maternal exposure to anti-androgenic compounds, vinclozolin, flutamide and procymidone, has no effects on spermatogenesis and DNA methylation in male rats of subsequent generations"}]},{"@id":"https://cir.nii.ac.jp/crid/1361418519150797440","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Genome-Wide Dna Methylation Profiling Using Infinium\n            <sup>®</sup>\n            Assay"}]},{"@id":"https://cir.nii.ac.jp/crid/1361418519677747456","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Epigenetic Transgenerational Actions of Endocrine Disruptors and Male Fertility"}]},{"@id":"https://cir.nii.ac.jp/crid/1361418519715155968","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing"}]},{"@id":"https://cir.nii.ac.jp/crid/1361981469988178304","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Optimized design and data analysis of tag-based cytosine methylation assays"}]},{"@id":"https://cir.nii.ac.jp/crid/1361981470885494784","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Dna Hypomethylation In Cancer Cells"}]},{"@id":"https://cir.nii.ac.jp/crid/1362262945914756864","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Brain region-specific methylation in the promoter of the murine oxytocin receptor gene is involved in its expression regulation"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544418550308352","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"A sensitive transcriptome analysis method that can detect unknown transcripts"}]},{"@id":"https://cir.nii.ac.jp/crid/1363107369073986432","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies"}]},{"@id":"https://cir.nii.ac.jp/crid/1363107371084217600","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Advances in Genome-Wide DNA Methylation Analysis"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388843859802752","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Analysis of DNA methylation reveals a partial reprogramming of the Müller glia genome during retina regeneration"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388844928737536","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Quantitative cDNA-AFLP analysis for genome-wide expression studies"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670318868005888","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"RNA fingerprinting and differential display using arbitrarily primed PCR"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670319321915008","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Environmental chemical exposures and human epigenetics"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670320649575168","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Genome-wide high throughput analysis of DNA methylation in eukaryotes"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670320872597504","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Analyzing the cancer methylome through targeted bisulfite sequencing"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951794182339200","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951795333073408","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Methylated DNA is over-represented in whole-genome bisulfite sequencing data"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233268800199168","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233269366665344","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Environmental epigenomics and disease susceptibility"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233270947330176","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis"}]},{"@id":"https://cir.nii.ac.jp/crid/1390002184853221888","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Exploring disease-specific methylated CpGs in human male genital abnormalities by using methylated-site display-amplified fragment length polymorphism (MSD-AFLP)"}]},{"@id":"https://cir.nii.ac.jp/crid/1390587682741588992","@type":"Article","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Modification of the MSD-AFLP Method for Detection of 5-Hydroxymethylcytosine and Its Application to NGS"}]},{"@id":"https://cir.nii.ac.jp/crid/2050870367059425536","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Does the prenatal bisphenol A exposure alter DNA methylation levels in the mouse hippocampus？ : an analysis using a high-sensitivity methylome technique"}]},{"@id":"https://cir.nii.ac.jp/crid/2051714791989554816","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Detection of dioxin-induced demethylation of mouse Cyp1a1 gene promoter by a new labeling method for short DNA fragments possessing 5'-methylcytosine at the end"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1186/s12867-017-0083-2"},{"@type":"KAKEN","@value":"PRODUCT-21637247"},{"@type":"KAKEN","@value":"PRODUCT-22530889"},{"@type":"KAKEN","@value":"PRODUCT-22547543"},{"@type":"KAKEN","@value":"PRODUCT-23017361"},{"@type":"OPENAIRE","@value":"doi_dedup___::62d7bf219af1650b351d805d0cc5ef21"},{"@type":"CROSSREF","@value":"10.1186/s41021-017-0089-5_references_DOI_TkmPpCWJzod7jQzKOzAlfmhJHlG"},{"@type":"CROSSREF","@value":"10.1262/jrd.2019-069_references_DOI_TkmPpCWJzod7jQzKOzAlfmhJHlG"},{"@type":"CROSSREF","@value":"10.3390/biom13030471_references_DOI_TkmPpCWJzod7jQzKOzAlfmhJHlG"},{"@type":"CROSSREF","@value":"10.1186/s41021-018-0099-y_references_DOI_TkmPpCWJzod7jQzKOzAlfmhJHlG"},{"@type":"CROSSREF","@value":"10.1248/bpbreports.8.6_150_references_DOI_TkmPpCWJzod7jQzKOzAlfmhJHlG"}]}