Dynamics of single-cell gene expression

Cellular behavior has traditionally been investigated by utilizing bulk‐scale methods that measure average values for a population of cells. Such population‐wide studies mask the behavior of individual cells and are often insufficient for characterizing biological processes in which cellular heterogeneity plays a key role. A unifying theme of many recent studies has been a focus on the development and utilization of single‐cell experimental techniques that are capable of probing key biological phenomena in individual living cells. Recently, novel information about gene expression dynamics has been obtained from single‐cell experiments that draw upon the unique capabilities of fluorescent reporter proteins.

[1]  S. Benzer,et al.  Induced synthesis of enzymes in bacteria analyzed at the cellular level. , 1953, Biochimica et biophysica acta.

[2]  A. Novick,et al.  ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON. , 1957, Proceedings of the National Academy of Sciences of the United States of America.

[3]  P. Maloney,et al.  Distribution of suboptimally induces -D-galactosidase in Escherichia coli. The enzyme content of individual cells. , 1973, Journal of molecular biology.

[4]  M. Savageau.  Comparison of classical and autogenous systems of regulation in inducible operons , 1974, Nature.

[5]  D. Koshland,et al.  Non-genetic individuality: chance in the single cell , 1976, Nature.

[6]  W. Schieve,et al.  Stochastic model of linear, continuous protein synthesis in bacterial populations. , 1977, Journal of theoretical biology.

[7]  S Falkow,et al.  FACS-optimized mutants of the green fluorescent protein (GFP). , 1996, Gene.

[8]  L. Poulsen,et al.  New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria , 1998, Applied and Environmental Microbiology.

[9]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.

[10]  M. Tatematsu,et al.  Isolation of Differentiated Squamous and Undifferentiated Spindle Carcinoma Cell Lines with Differing Metastatic Potential from a 4‐Nitroquinoline N‐Oxide‐induced Tongue Carcinoma in a F344 Rat , 2000, Japanese journal of cancer research : Gann.

[11]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[12]  G. Whitesides,et al.  Fabrication of microfluidic systems in poly(dimethylsiloxane) , 2000, Electrophoresis.

[13]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[14]  U Alon,et al.  Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[15]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[16]  S. Avery,et al.  Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry , 2000, Yeast.

[17]  B. Séraphin,et al.  Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion , 2001, The EMBO journal.

[18]  M. Thattai,et al.  Intrinsic noise in gene regulatory networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[19]  G. Whitesides,et al.  Generation of Gradients Having Complex Shapes Using Microfluidic Networks , 2001 .

[20]  U. Alon,et al.  Negative autoregulation speeds the response times of transcription networks. , 2002, Journal of molecular biology.

[21]  Jeff Hasty,et al.  Engineered gene circuits , 2002, Nature.

[22]  A. Hoffmann,et al.  The I (cid:1) B –NF-(cid:1) B Signaling Module: Temporal Control and Selective Gene Activation , 2022 .

[23]  C. Rao,et al.  Control, exploitation and tolerance of intracellular noise , 2002, Nature.

[24]  P. Swain,et al.  Intrinsic and extrinsic contributions to stochasticity in gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Ertugrul M. Ozbudak,et al.  Regulation of noise in the expression of a single gene , 2002, Nature Genetics.

[26]  A. Hoffmann,et al.  The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. , 2002, Science.

[27]  H. Mao,et al.  A microfluidic device with a linear temperature gradient for parallel and combinatorial measurements. , 2002, Journal of the American Chemical Society.

[28]  A. Goldbeter.  Computational approaches to cellular rhythms , 2002, Nature.

[29]  Atsushi Miyawaki,et al.  Lighting up cells: labelling proteins with fluorophores. , 2003, Nature cell biology.

[30]  S. Yamaguchi,et al.  Synchronization of Cellular Clocks in the Suprachiasmatic Nucleus , 2003, Science.

[31]  Thomas Henkel,et al.  Generation of larger numbers of separated microbial populations by cultivation in segmented-flow microdevices. , 2003, Lab on a chip.

[32]  M. Oren,et al.  The p53-Mdm2 module and the ubiquitin system. , 2003, Seminars in cancer biology.

[33]  Mads Kærn,et al.  Noise in eukaryotic gene expression , 2003, Nature.

[34]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[35]  S. Leibler,et al.  Bacterial Persistence as a Phenotypic Switch , 2004, Science.

[36]  Xavier Darzacq,et al.  Imaging gene expression in single living cells , 2004, Nature Reviews Molecular Cell Biology.

[37]  D B Kell,et al.  Oscillations in NF-kappaB signaling control the dynamics of gene expression. , 2004, Science.

[38]  Stanislas Leibler,et al.  Resilient circadian oscillator revealed in individual cyanobacteria , 2004, Nature.

[39]  A. Jayaraman,et al.  Dynamic gene expression profiling using a microfabricated living cell array. , 2004, Analytical chemistry.

[40]  Steve A. Kay,et al.  Bioluminescence Imaging of Individual Fibroblasts Reveals Persistent, Independently Phased Circadian Rhythms of Clock Gene Expression , 2004, Current Biology.

[41]  Uri Alon,et al.  Dynamics of the p53-Mdm2 feedback loop in individual cells , 2004, Nature Genetics.

[42]  J. Raser,et al.  Control of Stochasticity in Eukaryotic Gene Expression , 2004, Science.

[43]  James R. Johnson,et al.  Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression , 2004, Science.

[44]  P. Swain,et al.  Gene Regulation at the Single-Cell Level , 2005, Science.

[45]  M. Elowitz,et al.  Reconstruction of genetic circuits , 2005, Nature.

[46]  Nathan C Shaner,et al.  A guide to choosing fluorescent proteins , 2005, Nature Methods.

[47]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[48]  Jared E. Toettcher,et al.  Stochastic Gene Expression in a Lentiviral Positive-Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity , 2005, Cell.

[49]  J. Raser,et al.  Noise in Gene Expression: Origins, Consequences, and Control , 2005, Science.

[50]  J. Liao,et al.  A synthetic gene–metabolic oscillator , 2005, Nature.

[51]  D. Whitmore,et al.  Imaging of single light-responsive clock cells reveals fluctuating free-running periods , 2005, Nature Cell Biology.

[52]  C. Pesce,et al.  Regulated cell-to-cell variation in a cell-fate decision system , 2005, Nature.

[53]  E. Cox,et al.  Real-Time Kinetics of Gene Activity in Individual Bacteria , 2005, Cell.

[54]  A. van Oudenaarden,et al.  Noise Propagation in Gene Networks , 2005, Science.

[55]  B. Errede,et al.  A family of destabilized cyan fluorescent proteins as transcriptional reporters in S. cerevisiae , 2006, Yeast.

[56]  X. Xie,et al.  Probing Gene Expression in Live Cells, One Protein Molecule at a Time , 2006, Science.

[57]  J. Derisi,et al.  Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise , 2006, Nature.

[58]  M. L. Simpson,et al.  Gene network shaping of inherent noise spectra , 2006, Nature.

[59]  H Bolouri,et al.  Transcriptional noise and cellular heterogeneity in mammalian macrophages , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[60]  R. Singer,et al.  Transcriptional Pulsing of a Developmental Gene , 2006, Current Biology.

[61]  E. O’Shea,et al.  Noise in protein expression scales with natural protein abundance , 2006, Nature Genetics.

[62]  F. Cross,et al.  Coherence and timing of cell cycle start examined at single-cell resolution. , 2006, Molecular cell.

[63]  D. Volfson,et al.  Origins of extrinsic variability in eukaryotic gene expression , 2006, Nature.

[64]  R. Milo,et al.  Oscillations and variability in the p53 system , 2006, Molecular systems biology.

[65]  N. Friedman,et al.  Stochastic protein expression in individual cells at the single molecule level , 2006, Nature.

[66]  Uri Alon,et al.  A fluctuation method to quantify in vivo fluorescence data. , 2006, Biophysical journal.

[67]  Jeff Hasty,et al.  Monitoring dynamics of single-cell gene expression over multiple cell cycles , 2005, 2006 Bio Micro and Nanosystems Conference.

[68]  Nicholas J. Guido,et al.  A bottom-up approach to gene regulation , 2006, Nature.

[69]  Gürol M. Süel,et al.  An excitable gene regulatory circuit induces transient cellular differentiation , 2006, Nature.

[70]  Anne E Carpenter,et al.  Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins , 2006, Nature Methods.

[71]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , 2022 .