SELEX-seq: A method to determine DNA binding specificities of plant transcription factors

Abstract

Systematic evolution of ligands by exponential enrichment (SELEX) is a method that allows isolating specific nucleotide sequences that interact with a DNA binding protein of choice. By using a transcription factor (TF) and a randomized pool of double-stranded DNA, this technique can be used to characterize TF DNA binding specificities and affinities. The method is based on protein-DNA complex immunoprecipitation with protein-specific antibodies and subsequent DNA selection and amplification. Application of massively parallel sequencing (-seq) at each cycle of SELEX allows determining the relative affinities to any DNA sequence for any transcription factor or TF complex. The resulting TF DNA binding motifs can be used to predict potential DNA binding sites in genomes and thereby direct target genes of TFs.