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The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise.

Kempe H, Schwabe A, Crémazy F, Verschure PJ, Bruggeman FJ - Mol. Biol. Cell (2014)

Bottom Line: We compared three cell clones that differ only in the genomic integration site of an identical constitutively expressed reporter gene.We found that the cell-to-cell variability in the mRNA concentration is almost exclusively due to cell-to-cell variation in gene expression activity, whereas the cell-to-cell variation in mRNA number is larger, due to a significant contribution of cell volume variability.We concluded that the precise relationship between transcript number and cell volume sets the biological stochasticity of living cells.

View Article: PubMed Central - PubMed

Affiliation: Synthetic Systems Biology and Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

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Statistics of single-cell volumes. (A) Overview of the determination of the cell volumes. The background intensity was used to track the contour of the cell, and the DAPI signal provides the nuclear contour. The three-dimensional cell image was reconstructed by combining the contours of subsequent z-slices. (B) Statistics of the volumes of the cell (V), nucleus (VN), and cytoplasm (Vc) for the three different clones (color coded). Notation: μ = mean; σ = SD; cv = coefficient of variation; Δσ = the fraction of samples between μ – σ and μ + σ; ρ = correlation between mc and mN; and *p < 0.001 (H0: ρ = 0).The 95% confidence intervals of the statistics are given in Supplemental Figure S15. (C–E) Scatter plots of Vc and VN for the three different clones. Marginal histograms show the distribution of Vc (top) and VN (right). Supplemental Figure S5 gives the distributions of V. The measured number of cells is given by n.
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Figure 2: Statistics of single-cell volumes. (A) Overview of the determination of the cell volumes. The background intensity was used to track the contour of the cell, and the DAPI signal provides the nuclear contour. The three-dimensional cell image was reconstructed by combining the contours of subsequent z-slices. (B) Statistics of the volumes of the cell (V), nucleus (VN), and cytoplasm (Vc) for the three different clones (color coded). Notation: μ = mean; σ = SD; cv = coefficient of variation; Δσ = the fraction of samples between μ – σ and μ + σ; ρ = correlation between mc and mN; and *p < 0.001 (H0: ρ = 0).The 95% confidence intervals of the statistics are given in Supplemental Figure S15. (C–E) Scatter plots of Vc and VN for the three different clones. Marginal histograms show the distribution of Vc (top) and VN (right). Supplemental Figure S5 gives the distributions of V. The measured number of cells is given by n.

Mentions: To assess biological mRNA noise, we require, in addition to mRNA number per cell, the volume of each cell. The same confocal z-stack images used for smFISH were used to determine the whole-cell, cytoplasmic, and nuclear volumes of the cells by tracing the contours of these compartments (Figure 2A). This allows us to obtain mRNA number, volume, and concentration data for each cell.


The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise.

Kempe H, Schwabe A, Crémazy F, Verschure PJ, Bruggeman FJ - Mol. Biol. Cell (2014)

Statistics of single-cell volumes. (A) Overview of the determination of the cell volumes. The background intensity was used to track the contour of the cell, and the DAPI signal provides the nuclear contour. The three-dimensional cell image was reconstructed by combining the contours of subsequent z-slices. (B) Statistics of the volumes of the cell (V), nucleus (VN), and cytoplasm (Vc) for the three different clones (color coded). Notation: μ = mean; σ = SD; cv = coefficient of variation; Δσ = the fraction of samples between μ – σ and μ + σ; ρ = correlation between mc and mN; and *p < 0.001 (H0: ρ = 0).The 95% confidence intervals of the statistics are given in Supplemental Figure S15. (C–E) Scatter plots of Vc and VN for the three different clones. Marginal histograms show the distribution of Vc (top) and VN (right). Supplemental Figure S5 gives the distributions of V. The measured number of cells is given by n.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 2: Statistics of single-cell volumes. (A) Overview of the determination of the cell volumes. The background intensity was used to track the contour of the cell, and the DAPI signal provides the nuclear contour. The three-dimensional cell image was reconstructed by combining the contours of subsequent z-slices. (B) Statistics of the volumes of the cell (V), nucleus (VN), and cytoplasm (Vc) for the three different clones (color coded). Notation: μ = mean; σ = SD; cv = coefficient of variation; Δσ = the fraction of samples between μ – σ and μ + σ; ρ = correlation between mc and mN; and *p < 0.001 (H0: ρ = 0).The 95% confidence intervals of the statistics are given in Supplemental Figure S15. (C–E) Scatter plots of Vc and VN for the three different clones. Marginal histograms show the distribution of Vc (top) and VN (right). Supplemental Figure S5 gives the distributions of V. The measured number of cells is given by n.
Mentions: To assess biological mRNA noise, we require, in addition to mRNA number per cell, the volume of each cell. The same confocal z-stack images used for smFISH were used to determine the whole-cell, cytoplasmic, and nuclear volumes of the cells by tracing the contours of these compartments (Figure 2A). This allows us to obtain mRNA number, volume, and concentration data for each cell.

Bottom Line: We compared three cell clones that differ only in the genomic integration site of an identical constitutively expressed reporter gene.We found that the cell-to-cell variability in the mRNA concentration is almost exclusively due to cell-to-cell variation in gene expression activity, whereas the cell-to-cell variation in mRNA number is larger, due to a significant contribution of cell volume variability.We concluded that the precise relationship between transcript number and cell volume sets the biological stochasticity of living cells.

View Article: PubMed Central - PubMed

Affiliation: Synthetic Systems Biology and Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.

Show MeSH