Single-minded 1 and 2 are unique members of the basic helixloop-helix Per-Arnt-Sim family as they are transcriptional repressors. Here we report the identification and transcriptional characterization of mouse Sim2s, a splice variant of Sim2, which is missing the carboxyl Pro/Ala-rich repressive domain. Sim2s is expressed at high levels in kidney and skeletal muscle; however, the ratio of Sim2 to Sim2s mRNA differs between these tissues. Similar to full-length Sim2, Sim2s interacts with Arnt and to a lesser extent, Arnt2. The effects of Sim2s on transcriptional regulation through hypoxia, dioxin, and central midline response elements are different than that of full-length Sim2. Specifically, Sim2s exerts a less repressive effect on hypoxia-induced gene expression than full-length Sim2, but is just as effective as Sim2 at repressing TCDD-induced gene expression from a dioxin response element. Interestingly, Sim2s bind to and activates expression from a central midline response element-controlled reporter through an Arnt transactivation domain-dependent mechanism. The differences in expression pattern, protein interactions, and transcriptional activities between Sim2 and Sim2s may reflect differential roles each isoform plays during development or in tissue-specific effects on other proteinmediated pathways.The basic helix-loop-helix Per-Arnt-Sim (bHLH-PAS) 2 proteins comprise a growing family of transcription factors that play key roles during development and in sensing and adapting to changes in the environment. Individual PAS proteins are known to control morphogenesis, circadian rhythmicity, responses to hypoxia and toxin metabolism. These proteins contain a bHLH motif, which mediates dimerization with other bHLH proteins and contributes to determining DNA binding specificity. The PAS domain, named after the founding members of this family (period-arylhydrocarbon nuclear translocator-single minded), is a multifunctional protein surface responsible for such diverse activities as ligand binding, PAS protein dimerization, and non-PAS protein interactions (1).In addition to environmental adaptation, some members of the bHLH-PAS family regulate development. In Drosophila, single-minded (sim) acts as the master regulator of central nervous system midline development by controlling expression of many genes required for differentiation. Similar to other bHLH-PAS proteins, sim functions as a heterodimer with arnt (2). This complex binds to central midline elements (CME) in the regulatory regions of target genes to activate expression of proteins required for proper central midline establishment (2, 3).Two mammalian homologs of sim, Sim1 and Sim2, have been identified (4 -6). These proteins share a high degree of similarity in their PAS domains, but little conservation is apparent in their carboxyl termini. Sim1 and Sim2 interact with Arnt, but differ from Drosophila sim, the aryl hydrocarbon receptor (AHR) and hypoxia inducible factor (HIF) by functioning as transcriptional repressors (7, 8). Sim1 and Sim2 are expresse...