Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Identifieur interne : 002D46 ( Main/Exploration ); précédent : 002D45; suivant : 002D47Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Auteurs : Michael F. Berger [États-Unis] ; Anthony A. Philippakis ; Aaron M. Qureshi ; Fangxue S. He ; Preston W. Estep ; Martha L. BulykSource :
- Nature biotechnology [ 1087-0156 ] ; 2006.
Descripteurs français
- KwdFr :
- Animaux, Caenorhabditis elegans, Facteur de transcription EGR-1 (), Facteur de transcription Oct-1 (), Facteurs de transcription (), Facteurs de transcription (métabolisme), Facteurs de transcription à motifs basiques hélice-boucle-hélice et à glissière à leucines (), Humains, Liaison aux protéines, Protéines de Caenorhabditis elegans (), Protéines de Saccharomyces cerevisiae (), Protéines télomériques (), Protéines à homéodomaine (), Saccharomyces cerevisiae, Sites de fixation (physiologie), Souris, Séquençage par oligonucléotides en batterie ().
- MESH :
- métabolisme : Facteurs de transcription.
- physiologie : Sites de fixation.
- Animaux, Caenorhabditis elegans, Facteur de transcription EGR-1, Facteur de transcription Oct-1, Facteurs de transcription, Facteurs de transcription à motifs basiques hélice-boucle-hélice et à glissière à leucines, Humains, Liaison aux protéines, Protéines de Caenorhabditis elegans, Protéines de Saccharomyces cerevisiae, Protéines télomériques, Protéines à homéodomaine, Saccharomyces cerevisiae, Souris, Séquençage par oligonucléotides en batterie.
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
Affiliations:
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Le document en format XML
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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. 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Berger</name><affiliation wicri:level="1"><nlm:affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115</wicri:regionArea><wicri:noRegion>Massachusetts 02115</wicri:noRegion></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="KwdFr" xml:lang="fr"><term>Animaux</term><term>Caenorhabditis elegans</term><term>Facteur de transcription EGR-1 ()</term><term>Facteur de transcription Oct-1 ()</term><term>Facteurs de transcription ()</term><term>Facteurs de transcription (métabolisme)</term><term>Facteurs de transcription à motifs basiques hélice-boucle-hélice et à glissière à leucines ()</term><term>Humains</term><term>Liaison aux protéines</term><term>Protéines de Caenorhabditis elegans ()</term><term>Protéines de Saccharomyces cerevisiae ()</term><term>Protéines télomériques ()</term><term>Protéines à homéodomaine ()</term><term>Saccharomyces cerevisiae</term><term>Sites de fixation (physiologie)</term><term>Souris</term><term>Séquençage par oligonucléotides en batterie ()</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="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Sites de fixation</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><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Caenorhabditis elegans</term><term>Facteur de transcription EGR-1</term><term>Facteur de transcription Oct-1</term><term>Facteurs de transcription</term><term>Facteurs de transcription à motifs basiques hélice-boucle-hélice et à glissière à leucines</term><term>Humains</term><term>Liaison aux protéines</term><term>Protéines de Caenorhabditis elegans</term><term>Protéines de Saccharomyces cerevisiae</term><term>Protéines télomériques</term><term>Protéines à homéodomaine</term><term>Saccharomyces cerevisiae</term><term>Souris</term><term>Séquençage par oligonucléotides en batterie</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><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L" last="Bulyk">Martha L. Bulyk</name><name sortKey="Estep, Preston W" sort="Estep, Preston W" uniqKey="Estep P" first="Preston W" last="Estep">Preston W. Estep</name><name sortKey="He, Fangxue S" sort="He, Fangxue S" uniqKey="He F" first="Fangxue S" last="He">Fangxue S. He</name><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A" last="Philippakis">Anthony A. Philippakis</name><name sortKey="Qureshi, Aaron M" sort="Qureshi, Aaron M" uniqKey="Qureshi A" first="Aaron M" last="Qureshi">Aaron M. Qureshi</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F" last="Berger">Michael F. Berger</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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