The maize R2R3-MYB regulator C1 cooperates with the basic helixloop-helix (bHLH) factor R to activate the expression of anthocyanin biosynthetic genes coordinately. As is the case for other bHLH factors, R harbors several protein-protein interaction domains. Here we show that not the classical but rather a briefly extended R bHLH region forms homodimers that bind canonical G-box DNA motifs. This bHLH DNA-binding activity is abolished if the C-terminal ACT (aspartokinase, chorismate, and TyrA) domain is licensed to homodimerize. Then the bHLH remains in the monomeric form, allowing it to interact with R-interacting factor 1 (RIF1). In this configuration, the R-RIF1 complex is recruited to the promoters of a subset of anthocyanin biosynthetic genes, such as A1, through the interaction with its MYB partner C1. If, however, the ACT domain remains monomeric, the bHLH region dimerizes and binds to G-boxes present in several anthocyanin genes, such as Bz1. Our results provide a mechanism by which a dimerization domain in a bHLH factor behaves as a switch that permits distinct configurations of a regulatory complex to be tethered to different promoters. Such a combinatorial gene regulatory framework provides one mechanism by which genes lacking obviously conserved cis-regulatory elements are regulated coordinately.gene regulation | promoter switch T he evolution of multicellular organisms was accompanied by an increase in the complexity of gene-regulatory mechanisms, reflected in the expansion of transcription factor families and in the intricacy of the interactions between regulatory proteins and cis-regulatory elements in what is known today as "combinatorial transcriptional control." A premise of combinatorial control is that different arrangements of a discrete number of regulatory proteins can be used to regulate a much larger number of genes. Therefore, understanding how interactions between different regulatory proteins impact their ability to deploy the expression of specific gene sets is of fundamental biological importance.The basic helix-loop-helix (bHLH) family of transcription factors is among the largest in multicellular organisms (1). The hallmark of the family is a bHLH domain, which consists of two functionally distinct regions. Generally, the basic region of the bHLH domain directly contacts DNA harboring an E-box sequence (CANNTG), and the HLH region provides the potential for homo-and heterodimerization. In addition to the HLH motif, bHLH factors often contain additional protein-protein interaction domains. For example, members of the MYC family of mammalian cell proliferation regulators, such as MAD or MNT, contain a leucine-zipper (LZ) region that contributes to the selective interaction with MAX, another bHLH-LZ protein (2). MAX can form homo-or heterodimers with several related proteins, including MAD (3) and MNT (4). Providing a textbook example of combinatorial transcriptional control, MYC-MAX and MAX-MAX complexes bind E-boxes, but only the MYC-MAX heterodimer activates cell-proliferation gene...