Estimating DNA-Binding Specificities of Transcription Factors Using SELEX-Seq

Peilin Chen; Cezary Smaczniak; Johanna Haffner; Jose M Muino; Kerstin Kaufmann

doi:10.1007/978-1-0716-3354-0_10

Estimating DNA-Binding Specificities of Transcription Factors Using SELEX-Seq

Methods Mol Biol. 2023:2698:147-161. doi: 10.1007/978-1-0716-3354-0_10.

Authors

Peilin Chen¹, Cezary Smaczniak¹, Johanna Haffner¹, Jose M Muino¹, Kerstin Kaufmann²

Affiliations

¹ Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
² Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany. kerstin.kaufmann@hu-berlin.de.

PMID: 37682474
DOI: 10.1007/978-1-0716-3354-0_10

Abstract

Here we provide an updated protocol for the Systematic Evolution of Ligands followed by massively parallel sequencing (SELEX-seq) method to study protein-DNA interaction specificities. This in vitro method is used to characterize DNA-binding specificities of transcription factors (TFs). The procedure is based on cycles of immunoprecipitation of protein-DNA complexes, starting with a randomized DNA library of defined fragment length, followed by massively parallel sequencing. The updated protocol includes aspects of experimental design and procedure as well as basic instructions on data analysis.

Keywords: DNA-binding specificity; EMSA; Protein-DNA interactions; SELEX; Transcription factors.

MeSH terms

Data Analysis*
Gene Library
High-Throughput Nucleotide Sequencing
Immunoprecipitation
Transcription Factors* / genetics

Substances

Transcription Factors