Pair-rule-like transcription patterns during neural tube closure in a proto-vertebrate

Neural tube closure (NTC) is a conserved morphogenetic process in chordates in 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 these behaviors remain less understood. Here, we identify a transcriptional circuit involving Lmx1, Cdkn1b and Msx that regulates dorsal midline dynamics during NTC in the tunicate Ciona. High-resolution HCR in situ hybridization reveals that Lmx1 expression is dynamically enriched at the zippering point and advances in a posterior-to-anterior transcription wave, while Msx is downregulated in the same region, marking a transition from early neural patterning to morphogenesis. As closure progresses, Lmx1 and Cdkn1b exhibit complementary, alternating expression at the dorsal midline, resembling a pair-rule-like pattern. Misexpression experiments show that Lmx1 promotes proliferation and autoregulates, whereas Cdkn1b limits proliferation and impedes closure. Single-cell RNA-seq datasets reveal transcriptionally distinct dorsal neural populations enriched for Lmx1 or Cdkn1b. This transcriptional switch coordinates proliferation and fusion during NTC, suggesting a general strategy for regulating epithelial remodeling in animal embryos.