Fig. 4: Genomic distributions of licensing factors in WT and RIF1-KO cells.
a Representative ChIP-seq profiles of licensing factors (ORC1, ORC2, MCM2, MCM4), IZs, RNA-seq, protein-coding genes, and H3K9me3. Cells for ORC and MCM ChIP-seq were collected 4 h after release from nocodazole. ChIP-seq data are presented as input-normalised signal ratios. RNA-seq data are shown as Log2-transformed TPM. IZs are marked as green boxes. Protein-coding genes are depicted with arrows: red for forward strand, blue for reverse strand. b Metagene profiles of ORC1 and MCM4 enrichment. Genes are aligned at the transcription start site (TSS) and transcription termination site (TTS), with 100 kb extensions upstream of the TSS and downstream of the TTS. Genes are grouped into three categories based on expression level (TPM). c Representative MCM4 ChIP-seq profiles under control and RNA Polymerase II knockdown (Pol II KD) conditions. Data are shown as input-normalised signal ratios. RNA-seq profiles from control conditions are displayed below, with transcribed regions highlighted. d Metagene profiles of MCM4 ChIP-seq under control (solid line) and RNA Pol II KD (dotted line) conditions. Genes are categorised by transcription level (TPM) and aligned at the TSS and TTS, with 100 kb extensions upstream and downstream. e Representative ChIP-seq profiles of ORC1 and MCM4 in WT and RIF1-KO cells. Data are presented as input-normalised signal ratios. IZs from WT cells are indicated as green boxes. RNA-seq data from WT cells highlight transcribed regions, with genes shown as arrows. f Heatmaps showing ORC1, MCM2, and MCM4 enrichment in WT and RIF1-KO cells around IZs. IZs are grouped into five categories based on initiation timing and are centered with 100 kb flanking regions. Within each group, IZs are ordered by size. Aggregated enrichment profiles are plotted above each heatmap.
