The homeobox transcription factor MNX1 regulates the expression of many non-MN-specific neuronal genes in motor neurons

Motor neurons (MNs) control muscle movement and are essential for breathing, walking and fine motor skills. MN and Pancreas Homeobox 1 (MNX1) has long been recognized as a key marker of the MN lineage, and its deficiency in mice results in early postnatal lethality—likely by causing abnormal MN development and respiratory malfunction. However, its genome-wide targets and regulatory mechanism remain unresolved. Using an in vitro model for efficient MN induction, we identified ∼6000 MNX1-bound loci, of which half are conserved enhancers frequently overlap peaks for core MN-inducing factors ISL1 and LHX3. Despite its widespread binding, Mnx1 knockout affects only a few dozen bound loci and causes mis-regulation of ∼100 genes, the majority are up-regulated neuronal genes which routinely have comparable or even higher expression in brain relative to MNs. Integrative analysis predicts Pbx3 and Pou6f2 as two putative direct targets—both are homeobox genes highly expressed in the central nervous system, and adjacent to MNX1-repressed enhancers according to luciferase reporter assay. Collectively, our results suggest MNX1 restrains the expression of non-MN-specific neuronal genes, likely mainly through an indirect fashion. Further, the rarity of direct targets in contrast to widespread binding reflects a distinctive mode of transcriptional regulation.