Dynamical analysis on gene activity in the presence of repressors and an interfering promoter.

Transcription is regulated through interplay among transcription factors, an RNA polymerase (RNAP), and a promoter. Even for a simple repressive transcription factor that disturbs promoter activity at initial binding of RNAP, its repression level is not determined solely by the dissociation constant of transcription factor but is sensitive to timescales of processes in RNAP. We first analyze the promoter activity under strong repression by a slow binding repressor, in which case transcription events occur in bursts, followed by long quiescent periods while a repressor binds to the operator; the number of transcription events, bursting, and quiescent times are estimated by reaction rates. We then examine interference effect from an opposing promoter, using the correlation function of initiation events for a single promoter. The interference is shown to de-repress the promoter because RNAPs from the opposing promoter most likely encounter the repressor and remove it in case of strong repression. This de-repression mechanism should be especially prominent for the promoters that facilitate fast formation of open complex with the repressor whose binding rate is slower than approximately 1/s. Finally, we discuss possibility of this mechanism for high activity of promoter PR in the hyp-mutant of lambda-phage.

[1]  D. Steege,et al.  Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein. , 1990, The Journal of biological chemistry.

[2]  N. Proudfoot,et al.  Balancing transcriptional interference and initiation on the GAL7 promoter of Saccharomyces cerevisiae. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[3]  D. K. Hawley,et al.  Mechanism of activation of transcription initiation from the lambda PRM promoter. , 1982, Journal of molecular biology.

[4]  Diane K. Hawley,et al.  Mechanism of activation of transcription initiation from the λPRM promoter , 1982 .

[5]  K. Sneppen,et al.  Modelling transcriptional interference and DNA looping in gene regulation. , 2007, Journal of molecular biology.

[6]  D. Reines,et al.  Elongation factor SII-dependent transcription by RNA polymerase II through a sequence-specific DNA-binding protein. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[7]  L. Hsu,et al.  Promoter clearance and escape in prokaryotes. , 2002, Biochimica et biophysica acta.

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

[9]  Kim Sneppen,et al.  A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli. , 2005, Journal of molecular biology.

[10]  Kim Sneppen,et al.  Physics in molecular biology , 2005 .

[11]  J. W. Little,et al.  Robustness of a gene regulatory circuit , 1999, The EMBO journal.

[12]  Benno Müller-Hill,et al.  Four dimers of λ repressor bound to two suitably spaced pairs of λ operators form octamers and DNA loops over large distances , 1999, Current Biology.

[13]  H. Bujard,et al.  PL of coliphage lambda: an alternative solution for an efficient promoter. , 1988, The EMBO journal.

[14]  P. V. von Hippel,et al.  Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions. , 1981, Biochemistry.

[15]  N. Murray,et al.  Convergent transcription in bacteriophage lambda: interference with gene expression. , 1979, Journal of molecular biology.

[16]  W. McClure,et al.  Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps. , 1985, Biochemistry.

[17]  J. Collins,et al.  Combinatorial promoter design for engineering noisy gene expression , 2007, Proceedings of the National Academy of Sciences.

[18]  M. Ehrenberg,et al.  Activities of constitutive promoters in Escherichia coli. , 1999, Journal of molecular biology.

[19]  S. Heinemann,et al.  Mutants in the y region of bacteriophage lambda constitutive for repressor synthesis: their isolation and the characterization of the Hyp phenotype. , 1982, Gene.

[20]  B. Müller-Hill,et al.  Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. , 1999, Current biology : CB.

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

[22]  M Lanzer,et al.  Promoters largely determine the efficiency of repressor action. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Siddhartha Roy,et al.  Activation and Repression of Transcription by Differential Contact: Two Sides of a Coin* , 1998, The Journal of Biological Chemistry.

[24]  M. A. Shea,et al.  The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. , 1985, Journal of molecular biology.

[25]  P. V. von Hippel,et al.  Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. , 1981, Biochemistry.

[26]  M. Kashlev,et al.  Bacterial Polymerase and Yeast Polymerase II Use Similar Mechanisms for Transcription through Nucleosomes* , 2003, Journal of Biological Chemistry.

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

[28]  S. Adhya,et al.  Promoter occlusion: Transcription through a promoter may inhibit its activity , 1982, Cell.

[29]  M. Ptashne,et al.  Transcriptional activation by recruitment , 1997, Nature.

[30]  Ian B. Dodd,et al.  Cooperativity in long-range gene regulation by the λ CI repressor , 2004 .

[31]  K. Shearwin,et al.  Transcriptional interference between convergent promoters caused by elongation over the promoter. , 2004, Molecular cell.

[32]  P. Cook.  The organization of replication and transcription. , 1999, Science.

[33]  Kim Sneppen,et al.  The Generation of Promoter-Mediated Transcriptional Noise in Bacteria , 2008, PLoS Comput. Biol..

[34]  N. Proudfoot,et al.  Transcriptional collision between convergent genes in budding yeast , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Vitaly Epshtein,et al.  Transcription through the roadblocks: the role of RNA polymerase cooperation , 2003, The EMBO journal.

[36]  Asis Das,et al.  GreA and GreB proteins revive backtracked RNA polymerase in vivo by promoting transcript trimming , 2000, The EMBO journal.

[37]  J. Elf,et al.  Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell , 2007, Science.

[38]  X. Darzacq,et al.  In vivo dynamics of RNA polymerase II transcription , 2007, Nature Structural &Molecular Biology.

[39]  K. Sneppen,et al.  . s of t ] 1 9 O ct 2 00 0 Stability Puzzles in Phage λ , 2008 .

[40]  N. Murray,et al.  Convergent transcription in bacteriophage λ: Interference with gene expression☆ , 1979 .

[41]  Farren J. Isaacs,et al.  Phenotypic consequences of promoter-mediated transcriptional noise. , 2006, Molecular cell.

[42]  C. Georgopoulos,et al.  An IS4 transposition causes a 13-bp duplication of phage lambda DNA and results in the constitutive expression of the cI and cro gene products. , 1982, Gene.

[43]  H. Buc,et al.  A new target for CRP action at the malT promoter. , 1987, The EMBO journal.

[44]  M. Kashlev,et al.  Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. , 2002, Molecular cell.

[45]  J. Gralla,et al.  5' nucleotide heterogeneity and altered initiation of transcription at mutant lac promoters. , 1982, Journal of molecular biology.

[46]  D. Luse,et al.  Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. , 1991, Genes & development.