Human whole genome replication timing

Faithful transmission of genetic material to daughter cells involves a characteristic temporal order of DNA replication, which may play a signi?cant role in the inheritance of epigenetic states. We have developed a genome-scale approach—Repli-Seq—to map tempo- rally ordered replicating DNA using next-generation sequencing and applied it to study regional variation in human DNA replica- tion time across multiple human cell types. The method requires as few as 8000 cytometry-fractionated cells for a single analysis, and provides high-resolution replication patterns with respect to both cell-cycle time and genomic position. We ?nd that different cell types exhibit characteristic replication signatures that reveal a striking plasticity in regional replication time patterns covering at least 50% of the human genome. We have also identi?ed au- tosomal regions with marked biphasic replication timing that in- clude known regions of monoallelic expression as well as many previously uncharacterized domains. Comparison with high- resolution genome-wide pro?les of DNaseI sensitivity revealed that DNA replication typically initiates within foci of accessible chromatin comprising clustered DNaseI hypersensitive sites, and that replica- tion time is better correlated with chromatin accessibility than with gene expression. The data collectively provide a unique, genome- wide picture of the epigenetic compartmentalization of the human genome and suggest that cell-lineage speci?cation involves exten- sive reprogramming of replication timing patterns.