Genomic DNA for Repliseq: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced by using a Zymo DNA extractin kit. RNA for DRIPc-seq: cells were lyzed in proteinase K digestion buffer, and genomic DNA/RNA complex were extraced with a standard phenol/chlorofomr protocol. DNA was degraded during the library prep procedure, and the RNA molecules were prerved. We follow the published protocol, as indicated below, to construct the libraries. DRIPc-seq: https://www.nature.com/articles/s41596-019-0159-1 Repli-seq: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01983-8