A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific chromatin assembly that supersedes these constraints is required to configure the genome to guide gene expression changes that drive faithful lineage progression. Loss-of-function approaches in B cell precursors show that IKAROS assembles interactions across megabase distances in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries to assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains. Gain of function in epithelial cells confirms IKAROS’ ability to reconfigure chromatin architecture at multiple scales. Although the compaction of the Igκ locus required for genome editing represents a function of IKAROS unique to lymphocytes, the more general function to preconfigure the genome to support lineage-specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction. Display omitted •Cohesin loading at lymphoid enhancers by IKAROS supports formation of structural loops•IKAROS-bound enhancers override CTCF boundaries to assemble lineage-specific domains•IKAROS-based 3D contacts reach over heterochromatin to place domains into euchromatin•Igκ locus contraction in euchromatin relies on IKAROS-dependent enhancer contacts IKAROS mediates long-distance interactions both within and across domains and compartments to assemble a lineage-specific 3D genome organization required for immune cell development and function.