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SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics.

Identifieur interne : 000F67 ( PubMed/Curation ); précédent : 000F66; suivant : 000F68

SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics.

Auteurs : Dana Chen [Israël] ; Yaron Orenstein [Israël] ; Rada Golodnitsky [Israël] ; Michal Pellach [Israël] ; Dorit Avrahami [Israël] ; Chaim Wachtel [Israël] ; Avital Ovadia-Shochat [Israël] ; Hila Shir-Shapira [Israël] ; Adi Kedmi [Israël] ; Tamar Juven-Gershon [Israël] ; Ron Shamir [Israël] ; Doron Gerber [Israël]

Source :

Scientific reports [ 2045-2322 ] ; 2016.

RBID : pubmed:27628341

Descripteurs français

KwdFr :
- Analyse sur microréseau, Banque de gènes, Facteurs de transcription (métabolisme), Liaison aux protéines, Microfluidique (), Motifs nucléotidiques (génétique), Reproductibilité des résultats, Sites de fixation, Séquence nucléotidique, Taille d'échantillon, Technique SELEX ().
MESH :
- génétique : Motifs nucléotidiques.
- métabolisme : Facteurs de transcription.
- Analyse sur microréseau, Banque de gènes, Liaison aux protéines, Microfluidique, Reproductibilité des résultats, Sites de fixation, Séquence nucléotidique, Taille d'échantillon, Technique SELEX.

English descriptors

KwdEn :
- Base Sequence, Binding Sites, Gene Library, Microarray Analysis, Microfluidics (methods), Nucleotide Motifs (genetics), Protein Binding, Reproducibility of Results, SELEX Aptamer Technique (methods), Sample Size, Transcription Factors (metabolism).
MESH :
- chemical , metabolism : Transcription Factors.
- genetics : Nucleotide Motifs.
- methods : Microfluidics, SELEX Aptamer Technique.
- Base Sequence, Binding Sites, Gene Library, Microarray Analysis, Protein Binding, Reproducibility of Results, Sample Size.

Abstract

Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression.

DOI: 10.1038/srep33351
PubMed: 27628341

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<term>Binding Sites</term>
<term>Gene Library</term>
<term>Microarray Analysis</term>
<term>Microfluidics (methods)</term>
<term>Nucleotide Motifs (genetics)</term>
<term>Protein Binding</term>
<term>Reproducibility of Results</term>
<term>SELEX Aptamer Technique (methods)</term>
<term>Sample Size</term>
<term>Transcription Factors (metabolism)</term>
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<term>Facteurs de transcription (métabolisme)</term>
<term>Liaison aux protéines</term>
<term>Microfluidique ()</term>
<term>Motifs nucléotidiques (génétique)</term>
<term>Reproductibilité des résultats</term>
<term>Sites de fixation</term>
<term>Séquence nucléotidique</term>
<term>Taille d'échantillon</term>
<term>Technique SELEX ()</term>
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<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term>
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</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Microfluidics</term>
<term>SELEX Aptamer Technique</term>
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<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term>
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<term>Gene Library</term>
<term>Microarray Analysis</term>
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<term>Reproducibility of Results</term>
<term>Sample Size</term>
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<term>Banque de gènes</term>
<term>Liaison aux protéines</term>
<term>Microfluidique</term>
<term>Reproductibilité des résultats</term>
<term>Sites de fixation</term>
<term>Séquence nucléotidique</term>
<term>Taille d'échantillon</term>
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<front><div type="abstract" xml:lang="en">Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression.</div>
</front>
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<DateCompleted><Year>2018</Year>
<Month>06</Month>
<Day>04</Day>
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<DateRevised><Year>2018</Year>
<Month>11</Month>
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<Month>09</Month>
<Day>15</Day>
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<Abstract><AbstractText>Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName>
<ForeName>Dana</ForeName>
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<ForeName>Yaron</ForeName>
<Initials>Y</Initials>
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<ForeName>Rada</ForeName>
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<Author ValidYN="Y"><LastName>Wachtel</LastName>
<ForeName>Chaim</ForeName>
<Initials>C</Initials>
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<ForeName>Ron</ForeName>
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SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics.

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