Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Identifieur interne : 000471 ( Ncbi/Curation ); précédent : 000470; suivant : 000472Compact, 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
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pubmed:16998473Le document en format XML
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<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>
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<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>
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<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>
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<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term>
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<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>
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<term>Caenorhabditis elegans</term>
<term>Humans</term>
<term>Mice</term>
<term>Protein Binding</term>
<term>Saccharomyces cerevisiae</term>
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<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>
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<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>
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<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>
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