We profiled the genome-wide interactome of the co-repressor C-terminal binding protein 2 (CTBP2) in primary murine macrophages (BMDM) in vehicle and LPS conditions after 3 h of stimulation. We find that CTBP2 interacts with the transcription factors NF-κB and AP-1 and forms a corepressor complex that involves KDM1A, the NuRD complex and other co-repressors.