Fig. 3
From: Epigenetic instability caused by absence of CIZ1 drives transformation during quiescence cycles
Perturbation of the condensin complex. A Genes that relate to chromatin or DNA repair from the 33 I-DN CIZ1-dependent DREAM targets outlined in Additional file 7: Table S1. B Expression (mean TPM ± SEM) of Smc4 and Mre11a, before (cycling, Cy) and after (quiescence, Q), by SW (left) and CI (right). Similar data for all 33 I-DN genes is given in Additional file 1: Fig.S3. A gene is defined as significantly changed when the following thresholds are met -1 > log2(fold change) > 1 and q < 0.05. Significance indicators are ** -1 > log2(fold change) > 1 and q < 0.01, *** -1 > log2(fold change) > 1 and q < 0.001, ns denotes no significant difference. C Scatter plots comparing expression (mean TPM) in cycling WT and CIZ1-null cells, for all genes within high level GO terms chromosome organisation and DNA repair, plus two subordinate terms for each, as indicated. The grey line (y = x) illustrates no difference between WT and CIZ1-null cells and the red line is the best fit to the data calculated in excel, with the slope of the line indicated. A skew towards the y axis indicates a higher expression in CIZ1-null cycling cells. D As in C, for subunits of the condensin complex, the cohesin complex, the TOR complex, and the CDC73 PAF1 complex. Expression of the condensin subunit class is significantly affected by loss of CIZ1. E Mean TPM for all condensin subunits in WT (green) and CIZ1-null (blue) PEFs in the cycling state, normalised to WT, ± SEM. Smc2 and Smc4 are the two core subunits common to both condensin I and II. Individually, no subunit is significantly different between WT and CIZ1-null. F Whole cell lysates from WT and CIZ1-null cycling populations, female (top) and male (bottom), illustrating the total protein levels for SMC2, SMC4, and histone H3. Right, quantification showing mean for the 4 independent populations (2 female, 2 male) with individual values indicated. Results are compared by t-test (F) or the Wilcoxon’s signed ranked test (C, D) where ns denotes no significant difference, *p < 0.05, **p < 0.01, ***p < 0.001