SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics
Identifieur interne : 001028 ( Main/Exploration ); précédent : 001027; suivant : 001029SELMAP - 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.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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.
Url:
DOI: 10.1038/srep33351
PubMed: 27628341
PubMed Central: 5024299
Affiliations:
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strict</wicri:regionArea></affiliation></author><author><name sortKey="Orenstein, Yaron" sort="Orenstein, Yaron" uniqKey="Orenstein Y" first="Yaron" last="Orenstein">Yaron Orenstein</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Blavatnik School of Computer Science, Tel-Aviv University</institution>, Tel-Aviv, 69978,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Golodnitsky, Rada" sort="Golodnitsky, Rada" uniqKey="Golodnitsky R" first="Rada" last="Golodnitsky">Rada Golodnitsky</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Pellach, Michal" sort="Pellach, Michal" uniqKey="Pellach M" first="Michal" last="Pellach">Michal Pellach</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Avrahami, Dorit" sort="Avrahami, Dorit" uniqKey="Avrahami D" first="Dorit" last="Avrahami">Dorit Avrahami</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wachtel, Chaim" sort="Wachtel, Chaim" uniqKey="Wachtel C" first="Chaim" last="Wachtel">Chaim Wachtel</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ovadia Shochat, Avital" sort="Ovadia Shochat, Avital" uniqKey="Ovadia Shochat A" first="Avital" last="Ovadia-Shochat">Avital Ovadia-Shochat</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Shir Shapira, Hila" sort="Shir Shapira, Hila" uniqKey="Shir Shapira H" first="Hila" last="Shir-Shapira">Hila Shir-Shapira</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Kedmi, Adi" sort="Kedmi, Adi" uniqKey="Kedmi A" first="Adi" last="Kedmi">Adi Kedmi</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Juven Gershon, Tamar" sort="Juven Gershon, Tamar" uniqKey="Juven Gershon T" first="Tamar" last="Juven-Gershon">Tamar Juven-Gershon</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Shamir, Ron" sort="Shamir, Ron" uniqKey="Shamir R" first="Ron" last="Shamir">Ron Shamir</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Blavatnik School of Computer Science, Tel-Aviv University</institution>, Tel-Aviv, 69978,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Gerber, Doron" sort="Gerber, Doron" uniqKey="Gerber D" first="Doron" last="Gerber">Doron Gerber</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University</institution>, Ramat-Gan, 5290002,<country>Israel</country></nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><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></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse sur microréseau</term><term>Banque de gènes</term><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></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Nucleotide Motifs</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Motifs nucléotidiques</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Microfluidics</term><term>SELEX Aptamer Technique</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Binding Sites</term><term>Gene Library</term><term>Microarray Analysis</term><term>Protein Binding</term><term>Reproducibility of Results</term><term>Sample Size</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse sur microréseau</term><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><term>Technique SELEX</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Badis, G" uniqKey="Badis G">G. Badis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, H" uniqKey="Xu H">H. Xu</name></author><author><name sortKey="Morrical, S W" uniqKey="Morrical S">S. W. Morrical</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stormo, G D" uniqKey="Stormo G">G. D. Stormo</name></author><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y. Zhao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stormo, G D" uniqKey="Stormo G">G. D. Stormo</name></author><author><name sortKey="Fields, D S" uniqKey="Fields D">D. S. 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Preacher</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Israël</li></country></list><tree><country name="Israël"><noRegion><name sortKey="Chen, Dana" sort="Chen, Dana" uniqKey="Chen D" first="Dana" last="Chen">Dana Chen</name></noRegion><name sortKey="Avrahami, Dorit" sort="Avrahami, Dorit" uniqKey="Avrahami D" first="Dorit" last="Avrahami">Dorit Avrahami</name><name sortKey="Gerber, Doron" sort="Gerber, Doron" uniqKey="Gerber D" first="Doron" last="Gerber">Doron Gerber</name><name sortKey="Golodnitsky, Rada" sort="Golodnitsky, Rada" uniqKey="Golodnitsky R" first="Rada" last="Golodnitsky">Rada Golodnitsky</name><name sortKey="Juven Gershon, Tamar" sort="Juven Gershon, Tamar" uniqKey="Juven Gershon T" first="Tamar" last="Juven-Gershon">Tamar Juven-Gershon</name><name sortKey="Kedmi, Adi" sort="Kedmi, Adi" uniqKey="Kedmi A" first="Adi" last="Kedmi">Adi Kedmi</name><name sortKey="Orenstein, Yaron" sort="Orenstein, Yaron" uniqKey="Orenstein Y" first="Yaron" last="Orenstein">Yaron Orenstein</name><name sortKey="Ovadia Shochat, Avital" sort="Ovadia Shochat, Avital" uniqKey="Ovadia Shochat A" first="Avital" last="Ovadia-Shochat">Avital Ovadia-Shochat</name><name sortKey="Pellach, Michal" sort="Pellach, Michal" uniqKey="Pellach M" first="Michal" last="Pellach">Michal Pellach</name><name sortKey="Shamir, Ron" sort="Shamir, Ron" uniqKey="Shamir R" first="Ron" last="Shamir">Ron Shamir</name><name sortKey="Shir Shapira, Hila" sort="Shir Shapira, Hila" uniqKey="Shir Shapira H" first="Hila" last="Shir-Shapira">Hila Shir-Shapira</name><name sortKey="Wachtel, Chaim" sort="Wachtel, Chaim" uniqKey="Wachtel C" first="Chaim" last="Wachtel">Chaim Wachtel</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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