Fig. 2

Transcriptome analysis on entry to quiescence. A Schematic describing two strategies for inducing quiescence, serum withdrawal (SW, 24 h), and contact inhibition (CI, 7 days). B The number of transcription units significantly upregulated (log₂fc > 1, red) or downregulated (log₂fc < 1, purple) upon quiescence entry via SW or CI (FDR q < 0.05) for WT and CIZ1-null PEFs, showing a similar number in each class. C Venn diagrams showing the number of transcription units significantly changed upon entry to quiescence that are common to both quiescence methods, divided into those that go up or down, for WT (green) and CIZ1-null (blue) cells. For WT cells, this defines a murine core quiescence gene set. D Dot plots showing the significance of overlap with all 5916 Gene Ontology (GO) terms for the core quiescence gene sets in C. The most significant GO terms (purple) relate to the cell cycle and are returned by the downregulated genes for both genotypes. E Median expression level (TPM) of upregulated and downregulated genes shown in B, for cycling and quiescent WT and CIZ1-null cells. F Heat maps compare expression (log₂(fold change)) during quiescence entry between WT and CIZ1-null PEFs, for the two quiescent methods. Transcription units are ordered by WT log₂(fold change) SW or CI; upregulated (red), downregulated (purple), and where q > 0.05 (white). G Venn diagrams illustrating CIZ1-dependent genes that are upregulated and downregulated during quiescence entry (intersection shows those that are not CIZ1-dependent). Genes on the left (green) change in WT cells only and are referred to as genes that “fail” (F) to change in CIZ1-null; genes on the right (blue) change in CIZ1-null cells only and are referred to as genes that are “inappropriately” (I) changed in CIZ1-null cells. Right, histogram showing the overlap between the two quiescence methods for CIZ1-dependent genes (F-UP; fail to go up, F-DN; fail to go down, I-UP; inappropriately up, I-DN; inappropriately down), highlighted in shades of brown. H Dot plot showing the significance of overlap between the four core CIZ1-dependent gene sets with 4762 GSEA Curated Gene Sets. I-DN (dark brown) overlap most significantly with Fischer DREAM Targets (systematic name M149). The 5 gene sets circled are further analysed in Additional file 6: SDataset 5. I Heat maps of all 844 DREAM complex target genes defined in M149 [3], showing expression (log₂(fold change)) during quiescence entry in WT and CIZ1-null PEFs, for the two quiescent methods. Genes are ordered by WT log₂(fold change) SW or CI, for both WT and CIZ1-null cells, so that differences in behaviour can be visualised