Promoter Sequence Determines the Relationship between Expression Level and Noise

A single transcription factor can activate or repress expression by three different mechanisms: one that increases cell-to-cell variability in target gene expression (noise) and two that decrease noise.

[1]  Paul J. Choi,et al.  Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells , 2010, Science.

[2]  T. Kepler,et al.  Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. , 2001, Biophysical journal.

[3]  Tsz-Leung To,et al.  Noise Can Induce Bimodality in Positive Transcriptional Feedback Loops Without Bistability , 2010, Science.

[4]  E. O’Shea,et al.  Living with noisy genes: how cells function reliably with inherent variability in gene expression. , 2007, Annual review of biophysics and biomolecular structure.

[5]  M. Newton,et al.  Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae , 2008, BMC Genomics.

[6]  Mads Kærn,et al.  Predictable trends in protein noise , 2006, Nature Genetics.

[7]  F. Cross,et al.  Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. , 2010, Developmental cell.

[8]  A. Tong,et al.  Synthetic genetic array analysis in Saccharomyces cerevisiae. , 2006, Methods in molecular biology.

[9]  Leah M. Octavio,et al.  Epigenetic and Conventional Regulation Is Distributed among Activators of FLO11 Allowing Tuning of Population-Level Heterogeneity in Its Expression , 2009, PLoS genetics.

[10]  Nir Friedman,et al.  Linking stochastic dynamics to population distribution: an analytical framework of gene expression. , 2006, Physical review letters.

[11]  D. Stillman,et al.  The Zap1 transcriptional activator also acts as a repressor by binding downstream of the TATA box in ZRT2 , 2004, The EMBO journal.

[12]  R. Segev,et al.  GENERAL PROPERTIES OF THE TRANSCRIPTIONAL TIME-SERIES IN ESCHERICHIA COLI , 2011, Nature Genetics.

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

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

[15]  D. Dubnau,et al.  Noise in Gene Expression Determines Cell Fate in Bacillus subtilis , 2007, Science.

[16]  Klaus Aktories,et al.  Noise Can Induce Bimodality in Positive Transcriptional Feedback Loops Without Bistability , 2010 .

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

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

[19]  S. Leibler,et al.  Robustness in simple biochemical networks , 1997, Nature.

[20]  N. Barkai,et al.  Robustness of the BMP morphogen gradient in Drosophila embryonic patterning , 2022 .

[21]  Bin Wu,et al.  Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene , 2011, Science.

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

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

[24]  D. Winge,et al.  Repression of ADH1 and ADH3 during zinc deficiency by Zap1‐induced intergenic RNA transcripts , 2006, The EMBO journal.

[25]  Steven Hahn,et al.  Structure and mechanism of the RNA polymerase II transcription machinery , 2004, Nature Structural &Molecular Biology.

[26]  J. Collins,et al.  Tuning and controlling gene expression noise in synthetic gene networks , 2010, Nucleic acids research.

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

[28]  L. Mirny,et al.  Spatial effects on the speed and reliability of protein–DNA search , 2007, Nucleic acids research.

[29]  Jané Kondev,et al.  Transcriptional control of noise in gene expression , 2008, Proceedings of the National Academy of Sciences.

[30]  Nacho Molina,et al.  Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics , 2011, Science.

[31]  Jianzhi Zhang,et al.  Impact of gene expression noise on organismal fitness and the efficacy of natural selection , 2011, Proceedings of the National Academy of Sciences.

[32]  Antoine Buetti-Dinh,et al.  Control and signal processing by transcriptional interference , 2009, Molecular systems biology.

[33]  Alexander van Oudenaarden,et al.  Transcript counting in single cells reveals dynamics of rDNA transcription , 2010, Molecular systems biology.

[34]  D. Kirschner,et al.  A methodology for performing global uncertainty and sensitivity analysis in systems biology. , 2008, Journal of theoretical biology.

[35]  Yaniv Lubling,et al.  Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. , 2011, Genome research.

[36]  K. Shearwin,et al.  Transcriptional interference by RNA polymerase pausing and dislodgement of transcription factors , 2011, Transcription.

[37]  Justin A. Pruneski,et al.  Intergenic transcription causes repression by directing nucleosome assembly. , 2011, Genes & development.

[38]  F Sherman,et al.  mRNA sequences influencing translation and the selection of AUG initiator codons in the yeast Saccharomyces cerevisiae , 1996, Molecular microbiology.

[39]  Bryan J Venters,et al.  A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. , 2011, Molecular cell.

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

[41]  D. Tranchina,et al.  Stochastic mRNA Synthesis in Mammalian Cells , 2006, PLoS biology.

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

[43]  Rob Phillips,et al.  Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression , 2010, PLoS Comput. Biol..

[44]  D. Larson,et al.  Single-RNA counting reveals alternative modes of gene expression in yeast , 2008, Nature Structural &Molecular Biology.