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

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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number33351
JournalScientific Reports
Volume6
DOIs
StatePublished - 15 Sep 2016

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