B-ZIP transcription factors heterodimerize with dominant negative designs, termed A-ZIPs, in a dimerization specific manner and inhibit its ability to bind DNA. Different A-ZIPs produce unique phenotypes in vivo suggesting that they have distinct B-ZIP heterodimerization partners. However, the identification of the in vivo heterodimerization partners of different A-ZIPs remains problematic. To identify the in vivo heterodimerization partners, a chimeric protein containing two ubiquitin motifs at the N-terminal of the A-ZIP domain was designed. The presence of ubiquitin reduced the concentration of specific co-transfected B-ZIP proteins. The ubiquitin enhanced degradation of the B-ZIP heterodimeric partner is inhibited by the proteasome inhibitor MG-132. These ubiquitin tagged A-ZIP dominant negatives may be more active in vivo because their endogenous heterodimerization partners are degraded more efficiently. This may be a general strategy to identify protein interaction partners. Published by Elsevier Inc.