Open Access Research article

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts

José Viñuelas1, Gaël Kaneko12, Antoine Coulon3, Elodie Vallin1, Valérie Morin1, Camila Mejia-Pous1, Jean-Jacques Kupiec4, Guillaume Beslon2 and Olivier Gandrillon1*

Author Affiliations

1 Université de Lyon, Université Lyon 1, Centre de Génétique et de Physiologie Moléculaire et Cellulaire (CGPhiMC), CNRS UMR5534, F-69622 Lyon, France

2 Université de Lyon, INSA-Lyon, INRIA, Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), CNRS UMR5205, F-69621 Lyon, France

3 Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA

4 INSERM, Centre Cavaillès, Ecole Normale Supérieure, F-75005 Paris, France

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BMC Biology 2013, 11:15  doi:10.1186/1741-7007-11-15

Published: 25 February 2013

Additional files

Additional file 1:

Table S1. Identification by splinkerette PCR of the mCherry genomic insertion sites for six 6C2 cellular clones.

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Additional file 2:

Figure S1. Determination of the mCherry reporter mRNA and protein half-lives. (A) Quantitative reverse transcription PCR measurement of mCherry mRNA decay after actinomycin D treatment in two different clones of the 6C2 cell line. The best-fitting exponential curve (black line) was found by minimizing least squares (between exponential curve and biological data). The deduced mCherry mRNA half-life was 7 hours and 4 minutes (424 minutes). (B) Flow-cytometry measurement of mCherry protein fluorescence decay after cycloheximide treatment in two different clones of the 6C2 cell line. The best-fitting exponential curve (black line) was found by minimizing least squares (between exponential curve and biological data). The deduced mCherry protein half-life was 65 hours and 47 minutes (3,947 minutes). For both parts, ordinates are on a logarithmic scale.

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Additional file 3:

Figure S2. Exploration of model parameters based on a comparison of fluorescence distributions and SSA simulations. This figure is similar to the Figure 4 except that the selected parameter set had the highest (that is, worst) score (shown as a brown circle in the upper left part of the figure) of the best scores obtained.

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Additional file 4:

Table S2. mCherry transcription rates and mRNA levels for six cellular clones of the 6C2 cell line.

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Additional file 5:

Figure S3. Model simulation of the perturbation of chromatin dynamics by TSA treatment. This figure is similar to the Figure 6 except that the best new chromatin dynamics was computed from the parameter set which had the highest (that is, worst) score (shown as a brown circle in the panel (A) of Figure S2 in Additional file 3) of the best scores obtained.

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