Twist1 is a basic helix-loop-helix (bHLH) factor that plays an important role in limb development. Haploinsufficiency of Twist1 results in polydactyly via the inability of Twist1 to antagonistically regulate the related factor Hand2. The mechanism modulating Twist1-Hand2 antagonism is via phosphoregulation of conserved threonine and serine residues in helix I of the bHLH domain. Phosphoregulation alters the dimerization affinities for both proteins. Here we show that the expression of Twist1 and Twist1 phosphoregulation mutants results in distinct limb phenotypes in mice. In addition to dimer regulation, Twist1 phosphoregulation affects the DNA binding affinities of Twist1 in a partner-dependent and cis-element-dependent manner. In order to gain a better understanding of the specific Twist1 transcriptional complexes that function during limb morphogensis, we employ a series of Twist1-tethered dimers that include the known Twist1 partners, E12 and Hand2, as well as a tethered Twist1 homodimer. We show that these dimers behave in a manner similar to monomerically expressed bHLH factors and result in distinct limb phenotypes that correlate well with those observed from the limb expression of Twist1 and Twist1 phosphoregulation mutants. Taken together, this study shows that the Twist1 dimer affinity for a given partner can modulate the DNA binding affinity and that Twist1 dimer choice determines phenotypic outcome during limb development.Members of the Twist family of bHLH 2 proteins are evolutionarily conserved transcription factors that play fundamental roles in the normal development of a number of tissues, including extraembryonic membranes, teeth, jaw, heart, and limbs (1-3). Although bHLH/helix-loop-helix proteins can be organized into five groups, bHLH factors can be generally classified into two groups: the ubiquitously expressed E-proteins (class A) and the tissue-specific/restricted bHLH factors (class B) (for a review, see Ref. 4). The classic model for bHLH function is that a heterodimer containing a member from class A and a member from class B interacts via the amphipathic ␣-helices. This interaction juxtaposes the basic domains of both proteins, such that a DNA binding domain is formed that recognizes a DNA cis-element termed an E-box (CANNTG) (4). The requirement for class A/class B heterodimerization for many bHLH factors is well established, and in the case of the skeletal myogenic bHLH factors (MyoD1, Myogenin, Myf5, and Mrf4), heterodimerization is critical for proper biological function (4, 5). Other class B factors, such as members of the Twist family of bHLH proteins, not only function as heterodimers with E-proteins but can also form homodimers and heterodimers with other class B bHLH proteins (1-3, 6). It is thought that the control of bHLH dimerization is a mechanism that could control transcriptional response.Recently, we have shown that members of the Twist family of bHLH proteins contain an evolutionarily conserved threonine and serine within helix 1 that can be phosphoregulated by the a...