Single-Minded 1 (SIM1) is a member of the basic helix–loop– helix/Per-ARNT-SIM (bHLH/PAS) family of transcriptional regulators that possess diverse roles in development and homeostasis. SIM1 is essential for survival of neuroendocrine secretory cells of the hypothalamus, which are involved in regulation of the feeding response, and may also possess unknown roles in muscle and kidney development (Michaud, J.L. et al., 1998. Genes Dev. 12 (20), 3264–3275). A closely related family member, SIM2, is also critical for post-natal survival, and has been strongly implicated in development of prostate, pancreatic and colon tumours. Specifics of differential gene regulation between SIM1 and SIM2 have yet to be explored. We are attempting to identify direct target genes and coregulatory proteins of SIM1, of which none are yet identified. We have generated a range of brainand kidney-derived mammalian cell lines in which we are able to control SIM1 protein levels via doxycycline-inducible protein expression, or shRNA-mediated knockdown. These lines are being analysed by microarray to identify genes which respond to temporal changes in SIM1 expression. We also seek to identify SIM1-interacting proteins via purification of SIM1 protein complexes from mammalian cells, followed by mass spectrometry. Results obtained using these experimental approaches will be compared to those from similar experiments designed to elucidate SIM2 function, and may therefore provide insight into the critical gene expression programs SIM1 is effecting throughout development, as well as the means by which this transcription factor achieves target gene specificity in the broader context of the bHLH/PAS protein family.