Proteins that contain basic helix-loop-helix (bHLH) and Per-Arnt-Sim motifs (PAS) function as transcription factors. bHLH–PAS proteins exhibit essential and diverse functions throughout the body, from cell specification and differentiation in embryonic development to the proper function of organs like the brain and liver in adulthood. bHLH–PAS proteins are divided into two classes, which form heterodimers to regulate transcription. Class I bHLH–PAS proteins are typically activated in response to specific stimuli, while class II proteins are expressed more ubiquitously. Here, we discuss the general structure and functions of bHLH–PAS proteins throughout the animal kingdom, including family members that do not fit neatly into the class I-class II organization. We review heterodimerization between class I and class II bHLH–PAS proteins, binding partner selectivity and functional redundancy. Finally, we discuss the evolution of bHLH–PAS proteins, and why a class I protein essential for cardiovascular development in vertebrates like chicken and fish is absent from mammals.

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