Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine.
Identifieur interne : 001E30 ( PubMed/Curation ); précédent : 001E29; suivant : 001E31Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine.
Auteurs : Christopher L. Warren [États-Unis] ; Jianfei Zhao ; Kimberly Glass ; Vikas Rishi ; Aseem Z. Ansari ; Charles VinsonSource :
- Lab on a chip [ 1473-0189 ] ; 2012.
Descripteurs français
- KwdFr :
- 5-Méthyl-cytosine (immunologie), 5-Méthyl-cytosine (métabolisme), ADN (métabolisme), Anticorps (immunologie), Ilots CpG, Méthylation de l'ADN, Protéine de liaison à l'élément de réponse à l'AMP cyclique (génétique), Séquençage par oligonucléotides en batterie (instrumentation), Test de retard de migration électrophorétique (instrumentation).
- MESH :
- génétique : Protéine de liaison à l'élément de réponse à l'AMP cyclique.
- immunologie : 5-Méthyl-cytosine, Anticorps.
- métabolisme : 5-Méthyl-cytosine, ADN, Séquençage par oligonucléotides en batterie, Test de retard de migration électrophorétique.
- Ilots CpG, Méthylation de l'ADN.
English descriptors
- KwdEn :
- 5-Methylcytosine (immunology), 5-Methylcytosine (metabolism), Antibodies (immunology), CpG Islands, Cyclic AMP Response Element-Binding Protein (genetics), DNA (metabolism), DNA Methylation, Electrophoretic Mobility Shift Assay (instrumentation), Oligonucleotide Array Sequence Analysis (instrumentation).
- MESH :
- chemical , genetics : Cyclic AMP Response Element-Binding Protein.
- chemical , immunology : 5-Methylcytosine, Antibodies.
- chemical , metabolism : 5-Methylcytosine, DNA.
- instrumentation : Electrophoretic Mobility Shift Assay, Oligonucleotide Array Sequence Analysis.
- CpG Islands, DNA Methylation.
Abstract
We synthesized customized double-stranded DNA microarrays including methyl-5-cytosine at CpG dinucleotides and produced all 163,555 possible 8-mers (un-, hemi-, and di-methylated) to gain insight into how methylation affects transcription factor binding. An antibody to methyl-5-cytidine showed greater binding to the methylated DNA, demonstrating efficient incorporation of methyl-5-cytosine into the synthesized DNA. In contrast, binding of the transcription factor CREB was inhibited by CpG methylation. This platform represents a powerful new technology to evaluate the effect of DNA methylation on protein binding in any sequence context.
DOI: 10.1039/c1lc20698b
PubMed: 22139143
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Warren</name><affiliation wicri:level="1"><nlm:affiliation>McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706</wicri:regionArea></affiliation></author><author><name sortKey="Zhao, Jianfei" sort="Zhao, Jianfei" uniqKey="Zhao J" first="Jianfei" last="Zhao">Jianfei Zhao</name></author><author><name sortKey="Glass, Kimberly" sort="Glass, Kimberly" uniqKey="Glass K" first="Kimberly" last="Glass">Kimberly Glass</name></author><author><name sortKey="Rishi, Vikas" sort="Rishi, Vikas" uniqKey="Rishi V" first="Vikas" last="Rishi">Vikas Rishi</name></author><author><name sortKey="Ansari, Aseem Z" sort="Ansari, Aseem Z" uniqKey="Ansari A" first="Aseem Z" last="Ansari">Aseem Z. Ansari</name></author><author><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22139143</idno><idno type="pmid">22139143</idno><idno type="doi">10.1039/c1lc20698b</idno><idno type="wicri:Area/PubMed/Corpus">001E30</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001E30</idno><idno type="wicri:Area/PubMed/Curation">001E30</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001E30</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine.</title><author><name sortKey="Warren, Christopher L" sort="Warren, Christopher L" uniqKey="Warren C" first="Christopher L" last="Warren">Christopher L. Warren</name><affiliation wicri:level="1"><nlm:affiliation>McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706</wicri:regionArea></affiliation></author><author><name sortKey="Zhao, Jianfei" sort="Zhao, Jianfei" uniqKey="Zhao J" first="Jianfei" last="Zhao">Jianfei Zhao</name></author><author><name sortKey="Glass, Kimberly" sort="Glass, Kimberly" uniqKey="Glass K" first="Kimberly" last="Glass">Kimberly Glass</name></author><author><name sortKey="Rishi, Vikas" sort="Rishi, Vikas" uniqKey="Rishi V" first="Vikas" last="Rishi">Vikas Rishi</name></author><author><name sortKey="Ansari, Aseem Z" sort="Ansari, Aseem Z" uniqKey="Ansari A" first="Aseem Z" last="Ansari">Aseem Z. Ansari</name></author><author><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name></author></analytic><series><title level="j">Lab on a chip</title><idno type="eISSN">1473-0189</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>5-Methylcytosine (immunology)</term><term>5-Methylcytosine (metabolism)</term><term>Antibodies (immunology)</term><term>CpG Islands</term><term>Cyclic AMP Response Element-Binding Protein (genetics)</term><term>DNA (metabolism)</term><term>DNA Methylation</term><term>Electrophoretic Mobility Shift Assay (instrumentation)</term><term>Oligonucleotide Array Sequence Analysis (instrumentation)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>5-Méthyl-cytosine (immunologie)</term><term>5-Méthyl-cytosine (métabolisme)</term><term>ADN (métabolisme)</term><term>Anticorps (immunologie)</term><term>Ilots CpG</term><term>Méthylation de l'ADN</term><term>Protéine de liaison à l'élément de réponse à l'AMP cyclique (génétique)</term><term>Séquençage par oligonucléotides en batterie (instrumentation)</term><term>Test de retard de migration électrophorétique (instrumentation)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Cyclic AMP Response Element-Binding Protein</term></keywords><keywords scheme="MESH" type="chemical" qualifier="immunology" xml:lang="en"><term>5-Methylcytosine</term><term>Antibodies</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>5-Methylcytosine</term><term>DNA</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéine de liaison à l'élément de réponse à l'AMP cyclique</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>5-Méthyl-cytosine</term><term>Anticorps</term></keywords><keywords scheme="MESH" qualifier="instrumentation" xml:lang="en"><term>Electrophoretic Mobility Shift Assay</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>5-Méthyl-cytosine</term><term>ADN</term><term>Séquençage par oligonucléotides en batterie</term><term>Test de retard de migration électrophorétique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>CpG Islands</term><term>DNA Methylation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Ilots CpG</term><term>Méthylation de l'ADN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We synthesized customized double-stranded DNA microarrays including methyl-5-cytosine at CpG dinucleotides and produced all 163,555 possible 8-mers (un-, hemi-, and di-methylated) to gain insight into how methylation affects transcription factor binding. An antibody to methyl-5-cytidine showed greater binding to the methylated DNA, demonstrating efficient incorporation of methyl-5-cytosine into the synthesized DNA. In contrast, binding of the transcription factor CREB was inhibited by CpG methylation. This platform represents a powerful new technology to evaluate the effect of DNA methylation on protein binding in any sequence context.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22139143</PMID><DateCompleted><Year>2012</Year><Month>04</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1473-0189</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>2</Issue><PubDate><Year>2012</Year><Month>Jan</Month><Day>21</Day></PubDate></JournalIssue><Title>Lab on a chip</Title><ISOAbbreviation>Lab Chip</ISOAbbreviation></Journal><ArticleTitle>Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine.</ArticleTitle><Pagination><MedlinePgn>376-80</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1039/c1lc20698b</ELocationID><Abstract><AbstractText>We synthesized customized double-stranded DNA microarrays including methyl-5-cytosine at CpG dinucleotides and produced all 163,555 possible 8-mers (un-, hemi-, and di-methylated) to gain insight into how methylation affects transcription factor binding. An antibody to methyl-5-cytidine showed greater binding to the methylated DNA, demonstrating efficient incorporation of methyl-5-cytosine into the synthesized DNA. In contrast, binding of the transcription factor CREB was inhibited by CpG methylation. This platform represents a powerful new technology to evaluate the effect of DNA methylation on protein binding in any sequence context.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Warren</LastName><ForeName>Christopher L</ForeName><Initials>CL</Initials><AffiliationInfo><Affiliation>McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Jianfei</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Glass</LastName><ForeName>Kimberly</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Rishi</LastName><ForeName>Vikas</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Ansari</LastName><ForeName>Aseem Z</ForeName><Initials>AZ</Initials></Author><Author ValidYN="Y"><LastName>Vinson</LastName><ForeName>Charles</ForeName><Initials>C</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>T15LM007359</GrantID><Acronym>LM</Acronym><Agency>NLM NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM069420</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>T15 LM007359</GrantID><Acronym>LM</Acronym><Agency>NLM NIH HHS</Agency><Country>United States</Country></Grant><Grant><Agency>Intramural NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM069420</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D052060">Research Support, N.I.H., 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