Topoisomerases such as TOP1 and TOP2β regulate gene transcription in the developing and mature nervous system by interacting with RNA polymerase II. Topoisomerase-encoding genes are mutated in some people with autistic spectrum disorder (ASD), but their contribution to ASD is unknown. Using microarray analysis, King et al. show that inhibition of TOP1 and TOP2β reduces the expression of nearly all extremely long genes (>200 kb) in mouse cortical neurons, including some associated with ASD. These data suggest that compromised topoisomerase function might contribute to neurodevelopmental disorders such as ASD.