The balance between excitatory versus inhibitory neuron specification during development is crucial for sensory information processing in later life. The basic helix-loop-helix (bHLH) transcription factors Ascl1 and Ptf1a are crucial for establishing this specificity in the dorsal spinal cord, but how these two factors, which recognise a similiar DNA motif, can have opposite downstream effects is unclear. Now, on p. 2803, Jane Johnson and colleagues use chromatin immuno-precipitation sequencing (ChIP-Seq) and RNA-sequencing (RNA-Seq) to identify the precise target genes and DNA-binding motifs for both proteins in vivo using tissue from the developing mouse neural tube. The authors show that the downstream targets of Ascl1 and Ptf1a include many known homeodomain neuronal specification factors, but that the targets differ widely between the two proteins. Despite this distinction, Ascl1 and Ptf1a bind the same E-box motif; however, the authors show that Ptf1a also binds an additional motif where Ascl1 is not detected. This may explain, at least in part, some of the specificity achieved by Ptf1a. The authors also show that non-E-box motifs are enriched in Ascl1- and Ptf1a-bound regions, suggesting that cooperation from other transcription factors may further enhance this specificity.