Topologically associating domains are stable units of replication-timing regulation

Abstract

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 rearrangements2-7. 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 domains8,10. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale11,12.Moreover, attempts to reconcileTADs andLADs to replication-timing data have not revealed a common, underlying domain structure8,9,13. 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.