Lmx1a drives Cux2 expression in the cortical hem through activation of a conserved intronic enhancer

During neocortical development, neurons are produced by a diverse pool of neural progenitors. A subset of progenitors express the Cux2 gene and are fate restricted to produce certain neuronal subtypes; however, the upstream pathways that specify these progenitor fates remain unknown. To uncover the transcriptional networks that regulate Cux2 expression in the forebrain, we characterized a conserved Cux2 enhancer that recapitulates Cux2 expression specifically in the cortical hem. Using a bioinformatic approach, we identified putative transcription factor (TF)-binding sites for cortical hem-patterning TFs. We found that the homeobox TF Lmx1a can activate the Cux2 enhancer in vitro Furthermore, we showed that Lmx1a-binding sites were required for enhancer activity in the cortical hem in vivo Mis-expression of Lmx1a in hippocampal progenitors caused an increase in Cux2 enhancer activity outside the cortical hem. Finally, we compared several human enhancers with cortical hem-restricted activity and found that recurrent Lmx1a-binding sites are a top shared feature. Uncovering the network of TFs involved in regulating Cux2 expression will increase our understanding of the mechanisms pivotal in establishing Cux2 lineage fates in the developing forebrain.