title: SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics.
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.
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Dana
authors.initials: D
authors.lastname: Chen
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel.
authors.forename: Yaron
authors.initials: Y
authors.lastname: Orenstein
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Rada
authors.initials: R
authors.lastname: Golodnitsky
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Michal
authors.initials: M
authors.lastname: Pellach
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Dorit
authors.initials: D
authors.lastname: Avrahami
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Chaim
authors.initials: C
authors.lastname: Wachtel
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Avital
authors.initials: A
authors.lastname: Ovadia-Shochat
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Hila
authors.initials: H
authors.lastname: Shir-Shapira
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Adi
authors.initials: A
authors.lastname: Kedmi
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Tamar
authors.initials: T
authors.lastname: Juven-Gershon
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel.
authors.forename: Ron
authors.initials: R
authors.lastname: Shamir
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Doron
authors.initials: D
authors.lastname: Gerber
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D015723:Gene Library; D046228:Microarray Analysis; D044085:Microfluidics / Q000379:methods*; D059372:Nucleotide Motifs / Q000235:genetics; D011485:Protein Binding; D015203:Reproducibility of Results; D052156:SELEX Aptamer Technique / Q000379:methods*; D018401:Sample Size; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors