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Here, Taylor et al. investigated how distal regulatory elements control gene transcription and chromatin topology in lineage specification during development. Through allele-specific genome editing and chromatin interaction analyses of the Sox2 locus in mouse embryonic stem cells, they found a striking disconnection between transcriptional control and chromatin architecture, and traced nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletions have no effect on promoter–enhancer interaction frequencies or topological domain organization.