Fig. 5: Nucleus-cell coordination is primarily pairwise and nucleus area is a key mophological predictor for H3K27me3. | Communications Biology

Fig. 5: Nucleus-cell coordination is primarily pairwise and nucleus area is a key mophological predictor for H3K27me3.

From: Regulation of chromatin modifications through coordination of nucleus size and epithelial cell morphology heterogeneity

Fig. 5

A Schematic illustrating cytoplasmic and nuclear features used in morphological analyses. CV refers to coefficient of variation of DAPI intensity. B Prediction-measurement correlation with nucleus area. Axis range has been optimized to highlight differences between groups. Group titled “Cell Morph” refers to cell morphology illustrated in (A). GPR and CCA denote Gaussian process regression and canonical correlation analysis, respectively. C Principal component analysis biplot of cell morphology, nuclear morphology, and H3K27me3 levels. PC indicates principal component. D Prediction-measurement correlation for H3K27me3 levels. Groups titled “Cell Morph” and “Nuc Morph” refer to morphologies illustrated in (A). Nonlinearity group utilizes GPR model. E H3K27me3 level predicted using GPR versus measured level. Gray shaded band represents the GPR 95% confidence interval. Red dashed line denotes a perfect correlation (r = 1). N = 1080. F Illustration of measured H3K27me3 levels in MDCK cells (top) and predicted levels using GPR (bottom). Color bar indicates normalized H3K27me3 level. G H3K27me3 prediction-measurement correlation for control and DN-KASH (KASH) using nucleus area as the sole predictor. H H3K27me3 prediction-measurement correlation obtained using multi-linear regression. I H3K27me3 prediction-measurement obtained using GPR. J Predictor importance rank comparison scatter plot between control and KASH cells. Key morphological features for control and KASH samples are emphasized in fuchsia and cyan, respectively. Correlation measurements were conducted using N = 376, N = 335, and N = 446 cells for (B, D); N = 1277, N = 1346, and N = 1101 cells for the control condition in (G–I); and N = 1262, N = 1438, and N = 1147 cells for the KASH condition in (G–I). “ns'', *, **, ***, ****, refer to p ≥ 0.05,  < 0.05,  < 0.01,  < 0.001, and  < 0.0001, respectively. 3 biological replicates were used for (B–F), while 4 biological replicates were used for (G–J).

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