Topologically associating domains are stable units of replication-timing regulation

Eukaryotic chromosomesreplicate in a temporal order knownas the replication-timing program1. Inmammals, replication timing is celltype-specificwith at least half thegenomeswitching replicationtiming during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements^2-7. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs)^4,5,8,9. Recent Hi-Cmapping hasunveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains^8,10. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale^11,12.Moreover, attempts to reconcileTADs andLADs to replication-timing data have not revealed a common, underlying domain structure^8,9,13. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions andmap their positions in 18 human and 13mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacentTADsthat replicate at similar times obscure replication domainboundaries, largely accounting for thepreviously reported lack of alignment. Moreover, cell-type-specific replication timing ofTADspartitions the genome into twolarge-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timingwith developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.