Dysregulated DNA replication is associated with cancer development. DNA replication initiates from ~50,000 sites in each cell cycle. Genome-wide profiles of replication origins can be generated using various sequencing-based methods following different molecular capture strategies. No previous study has integrated the results from these different experiments to characterize the most reproducible origins or their association with the replication initiation factor, Origin Recognition Complex (ORC), known to be important for origin-specification. We conducted an integrative analysis of 98 human origin profiling datasets from four different techniques including NS-seq, Repli-seq, Rerep-seq and Bubble-seq, and identified a total of 1,460,610 origins in the human genome. Of these, only 0.12% (1,746) were high-confidence “shared origins” that were detected by all four techniques. Compared with all origins, the shared origins have higher GC content and overlap more with gene promoters, CTCF binding sites, transcription factor (TF) binding hotspots, G-quadruplex sites and activating histone marks. Only ~20% of the shared origins (343) overlap with known ORC binding sites. Despite the low overlap between shared origins and ORC binding sites, permutation tests suggest that the overlap between shared origins, ORC binding sites, R-loops and promoters are all significantly higher than random expectation. The variability in origin identification by different techniques and by same techniques in different groups suggests that replication origins are specified by highly variable stochastic events influenced by epigenetic variability.
Citation Format: Mengxue Tian, Zhenjia Wang, Chongzhi Zang, Zhangli Su, Etsuko Shibata, Yoshiyuki Shibata, Anindya Dutta. Integrative analysis of genome-wide DNA replication origins in human cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3174.