GSE114623
Identification of cis elements for temporal and spatial control of DNA replication [Repli-seq epha4]
DNA replication occurs in units of chromatin higher order organization (Topologically Associating Domains, or TADs; replication domains, or RDs), which self-organize in 3D into sub-nuclear compartments of early or late replicating chromatin. However, identification of cis-elements regulating replication timing (RT) and sub-nuclear compartments has been a major challenge in the field. Through an extensive series of CRISPR mediated deletion and inversions at a pluripotency associated domain (DppA2/4) in mouse embryonic stem cells (mESCs), we have identified cis-regulatory “early replication control elements” (ERCEs) that mediate early replication and A/B compartmentalization. We show that CTCF/cohesin loops, including the TAD boundaries, were dispensable, and multiple internal DNA segments were necessary for the domain's early replication in a partially redundant fashion. These segments were also sufficient to maintain early replication in the context of large inversions, irrespective of TAD boundaries. High-resolution capture Hi-C of this region revealed three sites of major contact that also displayed prominent chromatin features. Targeted deletion of all three contact points, which do not include the major mapped replication origins, caused a complete shift to late replication and association with compartment B, equivalent to the switch during lineage commitment. Individual and pair-wise deletions confirmed their partial redundancy and interdependency in giving rise to domain-wise RT patterns, and suggest the importance of long-range interactions. ERCEs are enriched in properties of strong or super-enhancers, and regulate gene expression, although transcription itself is not sufficient in driving early replication. In sum, our results have revealed the first cis-elements regulating the temporal and spatial control of DNA replication that is independent of transcription. Overall design: Genome-wide replication timing profiles.