A pair-rule-like transcription network coordinates neural tube closure in a proto-vertebrate

Neural tube closure (NTC) is a conserved morphogenetic process in chordates, during which the neural plate folds and fuses to form a closed neural tube. While the mechanical forces and signaling pathways governing NTC have been characterized in vertebrates, the transcriptional programs coordinating cell behaviors during closure remain less understood. Here, we identify a transcriptional circuit involvingLmx1, Cdkn1b, andMsxthat regulates dorsal midline dynamics during NTC in the tunicateCiona. High-resolution HCRin situhybridization reveals thatLmx1is dynamically enriched at the zippering point and advances in a posterior-to-anterior transcription wave, whileMsxis downregulated in the same region, marking a transition from early neural patterning to morphogenetic execution. As closure progresses,Lmx1andCdkn1bexhibit complementary, alternating expression at the dorsal midline, resembling a pair-rule-like pattern. Misexpression studies show thatLmx1promotes proliferation and activates its own expression, whereasCdkn1blimits proliferation and impedes closure. Single-cell RNA-seq reveals transcriptionally distinct dorsal neural populations enriched forLmx1orCdkn1b, supporting spatially organized cell-cycle states. These findings suggest that a transcriptional switch fromMsxtoLmx1, followed by spatially alternatingLmx1andCdkn1bactivity, coordinates proliferation and neural fold fusion during NTC. This mechanism may represent a general strategy for regulating epithelial remodeling in animal embryos.