LMX1B missense-perturbation of regulatory element footprints disrupt postnatal serotonergic forebrain axon arborization

Pathogenic coding mutations are prevalent in human neuronal transcription factors (TFs) but how they disrupt development is poorly understood. Lmx1b is a master transcriptional regulator of postmitotic serotonin (5-HT) neuron development; over two hundred pathogenic heterozygous mutations have been discovered in human LMX1B, yet their impact on brain development has not been investigated. Here, we developed mouse models with different LMX1B DNA-binding missense mutations. Missense heterozygosity effected highly specific deficits in the postnatal maturation of forebrain serotonin axon arbors, primarily in the hippocampus and motor cortex, which was associated with spatial memory defects. Digital Genomic Footprinting (DGF) revealed that missense heterozygosity caused complete loss of Lmx1b motif protection and chromatin accessibility at sites enriched for a distal active enhancer/active promoter histone signature and homeodomain binding motifs; at other bound Lmx1b motifs, varying levels of losses, gains or unchanged accessibility were found. The spectrum of footprint changes was strongly associated with synapse and axon genes. Lmx1b missense heterozygosity further caused wide disruption of Lmx1b-dependent regulatory networks comprising diverse TFs. These findings suggest Lmx1b missense heterozygosity forces complex dominant negative-like and hypomorphic perturbations on serotonergic regulatory element TF binding and accessibility. Our work illustrates the power of DGF for gaining insight into how TF missense mutations disrupt regulatory networks within neuronal epigenomes.