MeCP2 binding and genome–lamina reorganization precede long gene activation during mouse corticogenesis

During corticogenesis, neural gene expression is tightly coordinated by chromatin and epigenetic changes, whose misregulation can lead to neurodevelopmental disorders ^1–4 . The role of spatial genome organization—particularly interactions with the nuclear lamina—during these developmental programs remains poorly understood. Here, we combined in utero electroporation with scDam&T-seq to jointly profile genome–lamina contacts and transcriptomes in single cells of the mouse embryonic cortex. Interestingly, we find extensive genome–lamina reorganization during corticogenesis that is strongly biased towards long neuronal genes (≥100 kb), which are associated with neurodevelopmental disorders including autism spectrum disorder. Detachment of these genes frequently precedes transcriptional activation, positioning lamina disengagement as an early gene regulatory event. We identify the methyl CpG binding protein 2 (MeCP2)—mutated in Rett syndrome—as a candidate mediator of this process. MeCP2 binds lamina-associated, hydroxymethylated long genes before their repositioning, suggesting that MeCP2 may play a role in genome–lamina reorganization. These findings suggest a link between prevalent genome–lamina reorganization and MeCP2 regulation to ensure proper spatiotemporal activation of long neuronal genes during corticogenesis.