MeCP2 Represses the Activity of Topoisomerase IIb in Long Neuronal Genes [eTIP-Seq]

A unique signature of neuronal transcriptomes is the high expression of the longest genes in the genome (e.g. >100 kilobases). These genes encode proteins with essential functions in neuronal physiology, and disruption of long gene expression has been implicated in neurological disorders. DNA topoisomerases resolve topological constraints that arise on DNA and facilitate the expression of long genes in neurons. Conversely, methyl-CpG binding protein 2 (MeCP2), which is disrupted in Rett syndrome, can act as a transcriptional repressor to downregulate the expression of long genes. The molecular mechanisms underlying the regulation of long genes by these factors are not fully understood, however, and whether or not they directly influence each other is not known. Here, we identify a functional interaction between MeCP2 and Topoisomerase II-beta (TOP2b) in neurons. We show that MeCP2 and TOP2b physically interact in vivo and map protein sequences sufficient for their physical interaction in vitro. We profile TOP2b activity genome-wide in neurons and detect enrichment at regulatory regions and gene bodies of long neuronal genes, including long genes regulated by MeCP2. Further, we find that knockdown and overexpression of MeCP2 leads to altered TOP2b activity at MeCP2-regulated genes. Our findings uncover a mechanism by which MeCP2 inhibits the activity of TOP2b at long genes in neurons and suggest that this mechanism is disrupted in neurodevelopment disorders caused by mutation of MeCP2. Overall design: Etoposide-mediated topoisomerase immunoprecipitation DNA-sequencing (eTIP-seq) for TOP2b. eTIP-seq performed on 12 days in vitro (DIV12) cultured cortical neurons that were dissected from embryonic day 14.5 (E14.5) mouse pups that were untreated or transduced with lentivirus.