Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Identifieur interne : 002222 ( PubMed/Corpus ); précédent : 002221; suivant : 002223Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Auteurs : Michael F. Berger ; Anthony A. Philippakis ; Aaron M. Qureshi ; Fangxue S. He ; Preston W. Estep ; Martha L. BulykSource :
- Nature biotechnology [ 1087-0156 ] ; 2006.
English descriptors
- KwdEn :
- Animals, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (chemistry), Binding Sites (physiology), Caenorhabditis elegans, Caenorhabditis elegans Proteins (chemistry), Early Growth Response Protein 1 (chemistry), Homeodomain Proteins (chemistry), Humans, Mice, Octamer Transcription Factor-1 (chemistry), Oligonucleotide Array Sequence Analysis (methods), Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins (chemistry), Telomere-Binding Proteins (chemistry), Transcription Factors (chemistry), Transcription Factors (metabolism).
- MESH :
- chemical , chemistry : Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Caenorhabditis elegans Proteins, Early Growth Response Protein 1, Homeodomain Proteins, Octamer Transcription Factor-1, Saccharomyces cerevisiae Proteins, Telomere-Binding Proteins, Transcription Factors.
- chemical , metabolism : Transcription Factors.
- methods : Oligonucleotide Array Sequence Analysis.
- physiology : Binding Sites.
- Animals, Caenorhabditis elegans, Humans, Mice, Protein Binding, Saccharomyces cerevisiae.
Abstract
Transcription factors (TFs) interact with specific DNA regulatory sequences to control gene expression throughout myriad cellular processes. However, the DNA binding specificities of only a small fraction of TFs are sufficiently characterized to predict the sequences that they can and cannot bind. We present a maximally compact, synthetic DNA sequence design for protein binding microarray (PBM) experiments that represents all possible DNA sequence variants of a given length k (that is, all 'k-mers') on a single, universal microarray. We constructed such all k-mer microarrays covering all 10-base pair (bp) binding sites by converting high-density single-stranded oligonucleotide arrays to double-stranded (ds) DNA arrays. Using these microarrays we comprehensively determined the binding specificities over a full range of affinities for five TFs of different structural classes from yeast, worm, mouse and human. The unbiased coverage of all k-mers permits high-throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution.
DOI: 10.1038/nbt1246
PubMed: 16998473
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.</title><author><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F" last="Berger">Michael F. Berger</name><affiliation><nlm:affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A" last="Philippakis">Anthony A. Philippakis</name></author><author><name sortKey="Qureshi, Aaron M" sort="Qureshi, Aaron M" uniqKey="Qureshi A" first="Aaron M" last="Qureshi">Aaron M. Qureshi</name></author><author><name sortKey="He, Fangxue S" sort="He, Fangxue S" uniqKey="He F" first="Fangxue S" last="He">Fangxue S. He</name></author><author><name sortKey="Estep, Preston W" sort="Estep, Preston W" uniqKey="Estep P" first="Preston W" last="Estep">Preston W. Estep</name></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L" last="Bulyk">Martha L. Bulyk</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16998473</idno><idno type="pmid">16998473</idno><idno type="doi">10.1038/nbt1246</idno><idno type="wicri:Area/PubMed/Corpus">002222</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002222</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.</title><author><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F" last="Berger">Michael F. Berger</name><affiliation><nlm:affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A" last="Philippakis">Anthony A. Philippakis</name></author><author><name sortKey="Qureshi, Aaron M" sort="Qureshi, Aaron M" uniqKey="Qureshi A" first="Aaron M" last="Qureshi">Aaron M. Qureshi</name></author><author><name sortKey="He, Fangxue S" sort="He, Fangxue S" uniqKey="He F" first="Fangxue S" last="He">Fangxue S. He</name></author><author><name sortKey="Estep, Preston W" sort="Estep, Preston W" uniqKey="Estep P" first="Preston W" last="Estep">Preston W. Estep</name></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L" last="Bulyk">Martha L. Bulyk</name></author></analytic><series><title level="j">Nature biotechnology</title><idno type="ISSN">1087-0156</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (chemistry)</term><term>Binding Sites (physiology)</term><term>Caenorhabditis elegans</term><term>Caenorhabditis elegans Proteins (chemistry)</term><term>Early Growth Response Protein 1 (chemistry)</term><term>Homeodomain Proteins (chemistry)</term><term>Humans</term><term>Mice</term><term>Octamer Transcription Factor-1 (chemistry)</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Protein Binding</term><term>Saccharomyces cerevisiae</term><term>Saccharomyces cerevisiae Proteins (chemistry)</term><term>Telomere-Binding Proteins (chemistry)</term><term>Transcription Factors (chemistry)</term><term>Transcription Factors (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Basic Helix-Loop-Helix Leucine Zipper Transcription Factors</term><term>Caenorhabditis elegans Proteins</term><term>Early Growth Response Protein 1</term><term>Homeodomain Proteins</term><term>Octamer Transcription Factor-1</term><term>Saccharomyces cerevisiae Proteins</term><term>Telomere-Binding Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Binding Sites</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Caenorhabditis elegans</term><term>Humans</term><term>Mice</term><term>Protein Binding</term><term>Saccharomyces cerevisiae</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Transcription factors (TFs) interact with specific DNA regulatory sequences to control gene expression throughout myriad cellular processes. However, the DNA binding specificities of only a small fraction of TFs are sufficiently characterized to predict the sequences that they can and cannot bind. We present a maximally compact, synthetic DNA sequence design for protein binding microarray (PBM) experiments that represents all possible DNA sequence variants of a given length k (that is, all 'k-mers') on a single, universal microarray. We constructed such all k-mer microarrays covering all 10-base pair (bp) binding sites by converting high-density single-stranded oligonucleotide arrays to double-stranded (ds) DNA arrays. Using these microarrays we comprehensively determined the binding specificities over a full range of affinities for five TFs of different structural classes from yeast, worm, mouse and human. The unbiased coverage of all k-mers permits high-throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16998473</PMID><DateCompleted><Year>2006</Year><Month>12</Month><Day>28</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1087-0156</ISSN><JournalIssue CitedMedium="Print"><Volume>24</Volume><Issue>11</Issue><PubDate><Year>2006</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Nature biotechnology</Title><ISOAbbreviation>Nat. Biotechnol.</ISOAbbreviation></Journal><ArticleTitle>Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.</ArticleTitle><Pagination><MedlinePgn>1429-35</MedlinePgn></Pagination><Abstract><AbstractText>Transcription factors (TFs) interact with specific DNA regulatory sequences to control gene expression throughout myriad cellular processes. However, the DNA binding specificities of only a small fraction of TFs are sufficiently characterized to predict the sequences that they can and cannot bind. We present a maximally compact, synthetic DNA sequence design for protein binding microarray (PBM) experiments that represents all possible DNA sequence variants of a given length k (that is, all 'k-mers') on a single, universal microarray. We constructed such all k-mer microarrays covering all 10-base pair (bp) binding sites by converting high-density single-stranded oligonucleotide arrays to double-stranded (ds) DNA arrays. Using these microarrays we comprehensively determined the binding specificities over a full range of affinities for five TFs of different structural classes from yeast, worm, mouse and human. The unbiased coverage of all k-mers permits high-throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Berger</LastName><ForeName>Michael F</ForeName><Initials>MF</Initials><AffiliationInfo><Affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Philippakis</LastName><ForeName>Anthony A</ForeName><Initials>AA</Initials></Author><Author ValidYN="Y"><LastName>Qureshi</LastName><ForeName>Aaron M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>He</LastName><ForeName>Fangxue S</ForeName><Initials>FS</Initials></Author><Author ValidYN="Y"><LastName>Estep</LastName><ForeName>Preston W</ForeName><Initials>PW</Initials><Suffix>3rd</Suffix></Author><Author 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