Protocol for mapping murine transcription factor interactomes and composite motifs combining affinity purification mass spectrometry and ChIP-seq

Abstract

Mass spectrometry (MS)-based approaches have significantly advanced our ability to study protein interaction networks in an unbiased manner. Here, we present a protocol that uses affinity purification (AP)-MS to identify interaction partners of a biotinylated transcription factor of interest, isolated from primary murine T cells. The resulting interactome data are integrated with motif analyses from chromatin immunoprecipitation sequencing (ChIP-seq) experiments. This combined approach facilitates the concurrent identification of protein interactors and composite DNA motifs, with each dataset corroborating the findings of the other.