Stochastic fluctuations and distributed control of gene expression impact cellular memory

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  Corre, Guillaume ^a,b   Stockholm, Daniel ^a,b   Arnaud, Ophélie ^c   Kaneko, Gaël ^c,d   Viñuelas, José ^c   Yamagata, Yoshiaki ^f   Neildez Nguyen, Thi My Anh ^a,b   Kupiec, Jean Jacques ^e   Beslon, Guillaume ^d   Gandrillon, Olivier ^c   Paldi, András ^a,b   Macarthur, Ben D ^g  

^a INSERM   (France)

^b PSL RESEARCH UNIVERSITY   (France)

^c UNIVERSITÉ LYON 1   (France)

^d UNIVERSITÉ DE LYON   (France)

^e ECOLE NORMALE SUPÉRIEURE   (France)

^f YAMAGUCHI UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^g UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; CELL SELECTION; DAUGHTER CELL; EPIGENETICS; FLOW CYTOMETRY; GENE CONTROL; GENE EXPRESSION; GENE PRODUCT; GENETIC VARIABILITY; HUMAN; MEMORY; MOLECULAR CLONING; PHENOTYPE; PROTEIN EXPRESSION; PROTEIN STABILITY; REPORTER GENE; STATISTICS; ANIMAL EMBRYO; CELL LINEAGE; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PATHOLOGY; RETINOBLASTOMA; TUMOR CELL CULTURE;

CELL LINEAGE; COMPUTER SIMULATION; EMBRYO, MAMMALIAN; EPIGENOMICS; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, REPORTER; HUMANS; PHENOTYPE; RETINOBLASTOMA; STOCHASTIC PROCESSES; TRANSCRIPTION, GENETIC; TUMOR CELLS, CULTURED;

EID: 84919941146     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0115574     Document Type: Article

References (20)

1. Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451-464.
2. Levsky JM, Singer RH (2003) Gene expression and the myth of the average cell. Trends Cell Biol 13: 4-6.
3. Lestas I, Vinnicombe G, Paulsson J (2010) Fundamental limits on the suppression of molecular fluctuations. Nature 467: 174-178.
4. Balazsi G, van Oudenaarden A, Collins JJ (2011) Cellular decision making and biological noise: from microbes to mammals. Cell 144: 910-925.
5. Huang S (2009) Non-genetic heterogeneity of cells in development: more than just noise. Development 136: 3853-3862.
6. Huh D, Paulsson J (2011) Non-genetic heterogeneity from stochastic partitioning at cell division. Nat Genet 43: 95-100.
7. Vinuelas J, Kaneko G, Coulon A, Vallin E, Morin V, et al. (2013) Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts. BMC Biol 11: 15.
8. Neildez-Nguyen TM, Parisot A, Vignal C, Rameau P, Stockholm D, et al. (2008) Epigenetic gene expression noise and phenotypic diversification of clonal cell populations. Differentiation 76: 33-40.
9. Pedraza JM, Paulsson J (2008) Effects of molecular memory and bursting on fluctuations in gene expression. Science 319: 339-343.
10. Benjamin D, Colombi M, Stoecklin G, Moroni C (2006) A GFP-based assay for monitoring posttranscriptional regulation of ARE-mRNA turnover. Mol Biosyst 2: 561-567.
11. Kitsera N, Khobta A, Epe B (2007) Destabilized green fluorescent protein detects rapid removal of transcription blocks after genotoxic exposure. Biotechniques 43: 222-227.
12. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, et al. (2011) Global quantification of mammalian gene expression control. Nature 473: 337-342.
13. Vinayagam A, Zirin J, Roesel C, Hu Y, Yilmazel B, et al. (2014) Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods 11: 94-99.
14. Golubev A (2012) Genes at work in random bouts: Stochastically discontinuous gene activity makes cell cycle duration and cell fate decisions variable, thus providing for stem cells plasticity. Bioessays 34: 311- 319.
15. Schwanhausser B, Wolf J, Selbach M, Busse D (2013) Synthesis and degradation jointly determine the responsiveness of the cellular proteome. Bioessays 35: 597-601.
16. Fallaux FJ, Kranenburg O, Cramer SJ, Houweling A, Van Ormondt H, et al. (1996) Characterization of 911: A new helper cell line for the titration and propagation of early region 1-deleted adenoviral vectors. Hum Gene Ther 7: 215-222.
17. Uren AG, Mikkers H, Kool J, van der Weyden L, Lund AH, et al. (2009) A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites. Nat Protoc 4: 789- 798.
18. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, et al. (2006) CellProfiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7: R100.
19. Team RDCao (2005) R: A language and environment for statistical computing.
20. Wickham H (2009) ggplot2: Elegant Graphics for Data Analysis.