The Pbx1 and Meis1 proto-oncogenes code for divergent homeodomain proteins that are targets for oncogenic mutations in human and murine leukemias, respectively, and implicated by genetic analyses to functionally collaborate with Hox proteins during embryonic development and/or oncogenesis. Although Pbx proteins have been shown to dimerize with Hox proteins and modulate their DNA binding properties in vitro, the biochemical compositions of endogenous Pbx-containing complexes have not been determined. In the present study, we demonstrate that Pbx and Meis proteins form abundant complexes that comprise a major Pbx-containing DNA binding activity in nuclear extracts of cultured cells and mouse embryos. Pbx1 and Meis1 dimerize in solution and cooperatively bind bipartite DNA sequences consisting of directly adjacent Pbx and Meis half sites. Pbx1-Meis1 heterodimers display distinctive DNA binding specificities and cross-bind to a subset of Pbx-Hox sites, including those previously implicated as response elements for the execution of Pbx-dependent Hox programs in vivo. Chimeric oncoprotein E2a-Pbx1 is unable to bind DNA with Meis1, due to the deletion of amino-terminal Pbx1 sequences following fusion with E2a. We conclude that Meis proteins are preferred in vivo DNA binding partners for wild-type Pbx1, a relationship that is circumvented by its oncogenic counterpart E2a-Pbx1.Hox proteins make critical contributions to cell fate and segmental patterning during embryonic development (30). As targets of oncogenic mutations in human and murine leukemias, they are also implicated in cancer pathogenesis (3,4,21,34,35), which likely reflects perturbations of their roles in normal hematopoietic cell differentiation (23). In these capacities, they are presumed to function as transcription factors whose DNA binding activities are mediated through a conserved motif known as the homeodomain, which is structurally related to the bacterial helix-turn-helix motif (48). However, at a molecular level, the contributions of Hox proteins to developmental processes and disease pathogenesis are inadequately explained, given their disappointingly poor in vitro DNA binding affinities and specificities as monomeric proteins. This has led to the proposal that additional factors are required to modulate the DNA binding and transcriptional properties of Hox proteins (13), which would be consistent with models for achievement of specificity by other classes of transcriptional proteins.Genetic and biochemical studies support the argument for a role for members of the Pbx, exd, and ceh-20 subfamily (5) of divergent homeodomain proteins as potential Hox cofactors. In Drosophila melanogaster, exd is required for the execution of genetic programs that are also dependent on Hox proteins for appropriate segment-specific expression (40,45,46). A similar role for mammalian Pbx proteins is suggested by genetic analyses demonstrating that sequence elements with features of Pbx-Hox consensus sites are required for appropriate expression of murine Hoxb-1 in th...