The genomics of DNA replication of human chromosomes

Abstract

The sequencing of the human genome allows us to now address questions about DNA replication in human cells at a genome‐wide level on defined sequence fragments. The time of replication of mb of sequence clearly demarcates the chromosomes into domains of hundreds of kb with different epigenetic packaging. The time of replication also identifies chromosomal segments that show inter‐allelic variation in epigenetic packaging. Origin‐centered nascent strands were isolated from human cells by two independent methods: bromodeoxyuridine (BrdU) incorporation into nascent strands followed by immunoprecipitation with anti‐BrdU antibody or resistance of RNA‐capped nascent strand DNA to digestion by lambda exonuclease. On the 1% of the genome studied, about 80 sites (of a few hundred bases each) reproducibly yielded overlapping nascent strand peaks by both methods (high confidence origins). However, there are an additional >200 origins on the same 1% of the genome that occur at variable sites separated in location by up to 10 kb between nascent strand preparations. Thus, the origins that replicate our chromosomes are either site‐specific or plastic and the biochemical basis of the differences between the two types of origins will be interesting to explore.