Integrative analysis of DNA replication origins and ORC binding sites in human cells reveals a lack of overlap between them.

DNA replication initiates from ∼50,000 origins on human chromosomes in each cell-cycle and the origins are hypothesized to be specified by binding of factors like the Origin Recognition Complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and 5 ORC-binding site datasets to critically evaluate whether the most reproducible origins are specified by these features. Out of ∼7.5 million 300 bp chromosomal fragments reported to harbor origins by all the datasets, only 0.27% were reproducibly detected by four techniques (20,250 shared origins), suggesting extensive variability in origin usage and identification in different circumstances. 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF binding sites, G-quadruplex sites and activating histone marks, these overlaps are comparable or less than that of known Transcription Start Sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ∼13,000 reproducible ORC binding sites in human cancer cells, in contrast to the nearly 100% overlap between the two in the yeast, S. cerevisiae . Thus, in human cancer cell-lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and ORC-binding sites.