MeCP2 represses the activity of topoisomerase IIß in long neuronal genes.

A unique signature of neurons is the high expression of the longest genes in the genome. These genes have essential neuronal functions, and disruption of their expression has been implicated in neurological disorders. DNA topoisomerases resolve DNA topological constraints and facilitate neuronal long gene expression. Conversely, the Rett syndrome protein, methyl-CpG-binding protein 2 (MeCP2), can transcriptionally repress long genes. How these factors regulate long genes is not well understood, and whether they interact is not known. Here, we identify and map a functional interaction between MeCP2 and topoisomerase IIß (TOP2ß) in mouse neurons. We profile neuronal TOP2ß activity genome wide, detecting enrichment at regulatory regions and gene bodies of long genes, including MeCP2-regulated genes. We show that loss and overexpression of MeCP2 alter TOP2ß activity at MeCP2-regulated genes. These findings uncover a mechanism of TOP2ß inhibition by MeCP2 in neurons and implicate TOP2ß dysregulation in disorders caused by MeCP2 disruption.