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Stochastic fluctuations and distributed control of gene expression impact cellular memory.

Corre G, Stockholm D, Arnaud O, Kaneko G, Viñuelas J, Yamagata Y, Neildez-Nguyen TM, Kupiec JJ, Beslon G, Gandrillon O, Paldi A - PLoS ONE (2014)

Bottom Line: We compared cell clones with transgenes coding for highly stable mRNA and fluorescent proteins with clones expressing destabilized mRNA-s and proteins.Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations.These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.

View Article: PubMed Central - PubMed

Affiliation: Inserm, UMR 951, Université d'Evry Val d'Essonne, Genethon, Evry, F91002 France; Ecole Pratique des Hautes Etudes, Paris, France.

ABSTRACT
Despite the stochastic noise that characterizes all cellular processes the cells are able to maintain and transmit to their daughter cells the stable level of gene expression. In order to better understand this phenomenon, we investigated the temporal dynamics of gene expression variation using a double reporter gene model. We compared cell clones with transgenes coding for highly stable mRNA and fluorescent proteins with clones expressing destabilized mRNA-s and proteins. Both types of clones displayed strong heterogeneity of reporter gene expression levels. However, cells expressing stable gene products produced daughter cells with similar level of reporter proteins, while in cell clones with short mRNA and protein half-lives the epigenetic memory of the gene expression level was completely suppressed. Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations. These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.

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Related in: MedlinePlus

A snapshot from S2 Movie.The video shows cells expressing varying levels of fluorescence proteins spreading over the surface of the culture dish in a clonal population expressing the short half-lived fluorescent proteins. The YFP and CFP fluorescence was colored artificially in red and green for better visibility. It can be seen on the S2 Movie that there is no correlation between the fluorescence level of mother and daughter cells and there is no clear clustering of the cells with similar YFP/CFP ratio.
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pone-0115574-g008: A snapshot from S2 Movie.The video shows cells expressing varying levels of fluorescence proteins spreading over the surface of the culture dish in a clonal population expressing the short half-lived fluorescent proteins. The YFP and CFP fluorescence was colored artificially in red and green for better visibility. It can be seen on the S2 Movie that there is no correlation between the fluorescence level of mother and daughter cells and there is no clear clustering of the cells with similar YFP/CFP ratio.

Mentions: Many independent clones have been established. All of them displayed qualitatively similar fluctuating gene expression suggesting that the reporter gene's integration site did not impact significantly the temporal dynamics of fluctuations. Two representative clones with single insertion sites for both transgenes were analyzed in detail. As expected on the basis of the short half-life of the mRNA-s and proteins, the average level of YFP and CFP fluorescence measured by flow cytometry was found 100 times lower than the levels observed in cell clones with the stable proteins. Despite the large difference in the expression levels, the snapshot of the expression profile was similar in the two types of clones with cells that expressed only one fluorescent protein or that were negative for both. Time-lapse video microscopy analysis revealed that the fluorescence level of both reporter proteins now varied substantially and with a high frequency (Fig. 8 and S2 Movie). The period of the changes was shorter than the cell cycle, so that the same cell could change fluorescence between two divisions. A simple visual inspection was sufficient to conclude that no lineage-specific correlation of the fluorescence can be seen in these clones. On the basis of the time-lapse records we quantified the fluorescence fluctuations in about 120 cells from the two clones and calculated the autocorrelation functions for YFP and CFP in each cell and the time τ1/2 for the autocorrelation to drop to 50%. Although the cell-to-cell differences are important, both for YFP and CFP τ1/2 was less than 2 h in the majority of cells, illustrating the loss of the “cell memory” observed previously (Fig. 9). The half-life of the two proteins correlated well within the same cell suggesting that they are degraded through the same pathway (Fig. 9). Therefore, the rapid fluctuations of the fluorescence were made possible by the short lifetime of the mRNA-s and the corresponding fluorescent proteins and presumably directly reflect the fluctuations in the transcriptional activity of the genes.


Stochastic fluctuations and distributed control of gene expression impact cellular memory.

Corre G, Stockholm D, Arnaud O, Kaneko G, Viñuelas J, Yamagata Y, Neildez-Nguyen TM, Kupiec JJ, Beslon G, Gandrillon O, Paldi A - PLoS ONE (2014)

A snapshot from S2 Movie.The video shows cells expressing varying levels of fluorescence proteins spreading over the surface of the culture dish in a clonal population expressing the short half-lived fluorescent proteins. The YFP and CFP fluorescence was colored artificially in red and green for better visibility. It can be seen on the S2 Movie that there is no correlation between the fluorescence level of mother and daughter cells and there is no clear clustering of the cells with similar YFP/CFP ratio.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4274012&req=5

pone-0115574-g008: A snapshot from S2 Movie.The video shows cells expressing varying levels of fluorescence proteins spreading over the surface of the culture dish in a clonal population expressing the short half-lived fluorescent proteins. The YFP and CFP fluorescence was colored artificially in red and green for better visibility. It can be seen on the S2 Movie that there is no correlation between the fluorescence level of mother and daughter cells and there is no clear clustering of the cells with similar YFP/CFP ratio.
Mentions: Many independent clones have been established. All of them displayed qualitatively similar fluctuating gene expression suggesting that the reporter gene's integration site did not impact significantly the temporal dynamics of fluctuations. Two representative clones with single insertion sites for both transgenes were analyzed in detail. As expected on the basis of the short half-life of the mRNA-s and proteins, the average level of YFP and CFP fluorescence measured by flow cytometry was found 100 times lower than the levels observed in cell clones with the stable proteins. Despite the large difference in the expression levels, the snapshot of the expression profile was similar in the two types of clones with cells that expressed only one fluorescent protein or that were negative for both. Time-lapse video microscopy analysis revealed that the fluorescence level of both reporter proteins now varied substantially and with a high frequency (Fig. 8 and S2 Movie). The period of the changes was shorter than the cell cycle, so that the same cell could change fluorescence between two divisions. A simple visual inspection was sufficient to conclude that no lineage-specific correlation of the fluorescence can be seen in these clones. On the basis of the time-lapse records we quantified the fluorescence fluctuations in about 120 cells from the two clones and calculated the autocorrelation functions for YFP and CFP in each cell and the time τ1/2 for the autocorrelation to drop to 50%. Although the cell-to-cell differences are important, both for YFP and CFP τ1/2 was less than 2 h in the majority of cells, illustrating the loss of the “cell memory” observed previously (Fig. 9). The half-life of the two proteins correlated well within the same cell suggesting that they are degraded through the same pathway (Fig. 9). Therefore, the rapid fluctuations of the fluorescence were made possible by the short lifetime of the mRNA-s and the corresponding fluorescent proteins and presumably directly reflect the fluctuations in the transcriptional activity of the genes.

Bottom Line: We compared cell clones with transgenes coding for highly stable mRNA and fluorescent proteins with clones expressing destabilized mRNA-s and proteins.Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations.These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.

View Article: PubMed Central - PubMed

Affiliation: Inserm, UMR 951, Université d'Evry Val d'Essonne, Genethon, Evry, F91002 France; Ecole Pratique des Hautes Etudes, Paris, France.

ABSTRACT
Despite the stochastic noise that characterizes all cellular processes the cells are able to maintain and transmit to their daughter cells the stable level of gene expression. In order to better understand this phenomenon, we investigated the temporal dynamics of gene expression variation using a double reporter gene model. We compared cell clones with transgenes coding for highly stable mRNA and fluorescent proteins with clones expressing destabilized mRNA-s and proteins. Both types of clones displayed strong heterogeneity of reporter gene expression levels. However, cells expressing stable gene products produced daughter cells with similar level of reporter proteins, while in cell clones with short mRNA and protein half-lives the epigenetic memory of the gene expression level was completely suppressed. Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations. These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.

Show MeSH
Related in: MedlinePlus