Hominoid-specific transposable elements reshaped neural crest migration in craniofacial development

Craniofacial development is evolutionarily conserved, yet subtle changes in its regulatory network drive species-specific traits. Transposable elements (TEs) contribute to genome evolution, but their role in cranial neural crest cells (CNCCs) remains unclear. Here, we investigate the domestication of hominoid-specific TEs (LTR5Hs and SVAs) as enhancers during human CNCC specification, a process critical for vertebrate craniofacial development. Using human iPSC-derived CNCCs, we identified ~515 hominoid-specific TEs functioning as enhancers, including ~250 human-specific, predominantly LTR5Hs. These elements are enriched for CNCC coordinator motifs, are bound by the CNCC signature factor TWIST1, and their enhancer activity appears largely CNCC-specific. CRISPR-interference targeting ~75% of these active TEs led to widespread transcriptional dysregulation of genes involved in neural crest migration, and two orthogonal functional assays confirmed that CNCC migration is impaired upon TE repression. Finally, genes near human-specific TEs showed higher expression in human CNCCs compared to chimpanzee CNCCs, but TE repression restored gene expression to chimpanzee levels. These findings highlight how young TEs were domesticated to fine-tune CNCC regulatory networks, potentially contributing to lineage-specific craniofacial evolution. Overall design: RNA-seq of day 5 NCCs (5-day protocol) with and without gRNAs (2 replicates and 3 replicates respectively) ChIP-seq of day 5 NCCs (5-day protocol) with and without gRNAs (1 replicate each) ATAC-seq of day 5 NCCs (5-day protocol) with and without gRNAs (2 replicates each) ATAC-seq of day 18 NCCs (18-day protocol) with and without gRNAs (2 replicates each) ChIP-seq (H3k4me3) of day 5 NCCs (5-day protocol) with and without gRNAs (1 replicate each)