Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation (microarray)

Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation. Recruitment of transcription cofactors to 346 canonical TF binding sites and all possible single nucleotide variants was profiled. Three cofactors (BRD4, P300, and TBL1XR1) were profiled in three cell types (Jurkat, HEK293, and SUDHL4), and seven histone lyisne acetyltransferases (CBP, GCN5, MOF, MOZ, P300, PCAF, and TIP60) were profiled in both resting and 45 min TCR-stimulated Jurkat cells. All experiments were performed in duplicate or in triplicate.