Bifurcations in the interplay of messenger RNA, protein and nonprotein coding RNA

The interplay of messenger RNA (mRNA), protein, produced via translation of this RNA, and nonprotein coding RNA (ncRNA) may include regulation of the ncRNA production by protein and (i) ncRNA–protein association resulting in suppression of the protein regulatory activity or (ii) ncRNA–mRNA association resulting in degradation of the miRNA–mRNA complex. The kinetic models describing these two scenarios are found to predict bistability provided that protein suppresses the ncRNA formation.

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

[2]  P. Gammell.  MicroRNAs: recently discovered key regulators of proliferation and apoptosis in animal cells , 2007, Cytotechnology.

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

[4]  V. Zhdanov.  Oscillatory kinetics of gene transcription during cellular growth , 2007 .

[5]  V. Zhdanov.  Effect of mRNA diffusion on stochastic bursts in gene transcription , 2007 .

[6]  T. Hwa,et al.  Quantitative Characteristics of Gene Regulation by Small RNA , 2007, PLoS Biology.

[7]  V. Zhdanov.  Transient stochastic bistable kinetics of gene transcription during the cellular growth , 2006 .

[8]  F. Costa,et al.  Non-coding RNAs: new players in eukaryotic biology. , 2005, Gene.

[9]  J. Krebs,et al.  Noncoding but nonexpendable: transcriptional regulation by large noncoding RNA in eukaryotes. , 2007, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[10]  Yong Zhao,et al.  Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis , 2005, Nature.

[11]  Olaf Wolkenhauer,et al.  Intracellular delay limits cyclic changes in gene expression. , 2006, Mathematical biosciences.

[12]  F. Costa,et al.  Non-coding RNAs: lost in translation? , 2007, Gene.

[13]  Herbert Levine,et al.  Target-specific and global effectors in gene regulation by MicroRNA. , 2007, Biophysical journal.

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

[15]  Harvey F Lodish,et al.  Myogenic factors that regulate expression of muscle-specific microRNAs. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Andreas Radbruch,et al.  Transcriptional control networks of cell differentiation: insights from helper T lymphocytes. , 2004, Progress in biophysics and molecular biology.

[17]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[18]  Zhijun Duan,et al.  Epigenetic Regulation of Protein-Coding and MicroRNA Genes by the Gfi1-Interacting Tumor Suppressor PRDM5 , 2007, Molecular and Cellular Biology.

[19]  Samuel A. Isaacson,et al.  Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations , 2006, SIAM J. Sci. Comput..

[20]  Peter T Nelson,et al.  Energizing miRNA research: a review of the role of miRNAs in lipid metabolism, with a prediction that miR-103/107 regulates human metabolic pathways. , 2007, Molecular genetics and metabolism.

[21]  T. Misteli.  Physiological importance of RNA and protein mobility in the cell nucleus , 2007, Histochemistry and Cell Biology.

[22]  G. Friedlander,et al.  Regulation of gene expression by small non-coding RNAs: a quantitative view , 2007, Molecular systems biology.

[23]  V. Zhdanov.  Interplay of master regulatory proteins and mRNA in gene expression: 3D Monte Carlo simulations , 2008 .

[24]  Vladimir P. Zhdanov,et al.  Kinetic oscillations in the expression of messenger RNA, regulatory protein, and nonprotein coding RNA , 2008 .

[25]  D. Volfson,et al.  Delay-induced stochastic oscillations in gene regulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Hannah H. Chang,et al.  Multistable and multistep dynamics in neutrophil differentiation , 2006, BMC Cell Biology.

[27]  D. Reidel,et al.  The Transcriptional Landscape of the Mammalian Genome The FANTOM Consortium* and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)* , 2005 .

[28]  M. Sasai,et al.  Roles of noise in single and coupled multiple genetic oscillators. , 2007, The Journal of chemical physics.

[29]  Sui Huang,et al.  Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. , 2007, Developmental biology.

[30]  K. Sneppen,et al.  Efficient degradation and expression prioritization with small RNAs , 2006, Physical biology.

[31]  Thomas E. Royce,et al.  Global Identification of Human Transcribed Sequences with Genome Tiling Arrays , 2004, Science.

[32]  Stefan Bornholdt,et al.  Less Is More in Modeling Large Genetic Networks , 2005, Science.

[33]  M. Ferracin,et al.  Regulation of microRNA Expression: the Hypoxic Component , 2007, Cell cycle.

[34]  Alexander van Oudenaarden,et al.  Stochastic Gene Expression: from Single Molecules to the Proteome This Review Comes from a Themed Issue on Chromosomes and Expression Mechanisms Edited Measuring Noise Mrna Fluctuations , 2022 .

[35]  J. Goodrich,et al.  Non-coding-RNA regulators of RNA polymerase II transcription , 2006, Nature Reviews Molecular Cell Biology.

[36]  Peter T. McHale,et al.  Small Regulatory RNAs May Sharpen Spatial Expression Patterns , 2007, PLoS Comput. Biol..

[37]  P. Michalak,et al.  RNA world – the dark matter of evolutionary genomics , 2006, Journal of evolutionary biology.

[38]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.