Hansen-Stam Repli-Seq
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.