Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells

Rett syndrome may be treated by reactivating the silent copy of Mecp2 from the inactive X chromosome in female cells. Most studies that model Mecp2 reactivation have used mouse fibroblasts rather than neural cells, which would be critical for phenotypic reversal, and rely on fluorescent reporters that lack adequate sensitivity. Here, we present a mouse model based on a dual bioluminescent and fluorescent reporter to assess the level of reactivation of Mecp2 and the inactive X chromosome by treating neural stem cells with 5-azacytidine and Xist knockdown. We show that reactivation of Mecp2 and other X-linked genes correlates with CpG density, with distance from escapees, and, very strongly, with the presence of short interspersed nuclear elements. In addition, X-linked genes reactivated in neural stem cells overlap substantially with early reactivating genes by induced pluripotent stem cell reprogramming of fibroblasts or neuronal progenitors, indicating that X chromosome reactivation follows similar paths regardless of the technique or cell type used. •Xist knockdown and 5-Aza treatment lead to Mecp2 reactivation in neural stem cells•· SINE density and gene activity are potent indicators of X-linked gene reactivation•Genes reactivated in different cell types by different means overlap considerably In this article, Hegias Mira-Bontenbal, Joost Gribnau, and colleagues show that SINEs and activity signatures on the active X chromosome are strong predictors of X-linked gene reactivation from the inactive X in mouse neural stem cells. Different mechanisms to reactivate the X lead to a similar pool of reactivated genes in different cell types, implying a general path to reactivation.