Crossref journal-article
Elsevier BV
Biophysical Journal (78)
Bibliography

Voliotis, M., Cohen, N., Molina-París, C., & Liverpool, T. B. (2008). Fluctuations, Pauses, and Backtracking in DNA Transcription. Biophysical Journal, 94(2), 334–348.

Authors 4
  1. Margaritis Voliotis (first)
  2. Netta Cohen (additional)
  3. Carmen Molina-París (additional)
  4. Tanniemola B. Liverpool (additional)
References 63 Referenced 85
  1. {'year': '1944', 'series-title': 'What is Life?', 'author': 'Schrödinger', 'key': '10.1529/biophysj.107.105767_bib1'} / What is Life? by Schrödinger (1944)
  2. 10.1038/nature02257 / Nature / Summing up the noise in gene networks by Paulsson (2004)
  3. 10.1016/j.plrev.2005.03.003 / Phys. Life Rev. / Models of stochastic gene expression by Paulsson (2005)
  4. 10.1038/nrg1615 / Nat. Rev. Gen. / Stochasticity in gene expression: from theories to phenotypes by Kærn (2005)
  5. 10.1126/science.1070919 / Science / Stochastic gene expression in a single cell by Elowitz (2002)
  6. 10.1126/science.1109090 / Science / Noise propagation in gene networks by Pedraza (2005)
  7. 10.1126/science.1119623 / Science / Probing gene expression in live cells, one protein molecule at a time by Yu (2006)
  8. 10.1038/nrm1588 / Nat. Rev. Mol. Cell Biol. / Thinking quantitatively about transcriptional regulation by Greive (2005)
  9. 10.1073/pnas.88.6.2307 / Proc. Natl. Acad. Sci. USA / Transcription elongation and termination are competitive kinetic processes by von Hippel (1991)
  10. 10.1063/1.2213613 / Chaos / Noise in genetic and neural networks by Swain (2006)
  11. 10.1016/j.cell.2005.09.031 / Cell / Real-time kinetics of gene activity in individual bacteria by Golding (2005)
  12. 10.1146/annurev.biophys.35.010406.150153 / Annu. Rev. Biophys. Biomol. Struct. / Single-molecule analysis of RNA polymerase transcription by Bai (2006)
  13. 10.1073/pnas.0230489100 / Proc. Natl. Acad. Sci. USA / Sequence information can be obtained from single DNA molecules by Braslavsky (2003)
  14. 10.1016/0022-2836(84)90262-6 / J. Mol. Biol. / Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter by Malan (1984)
  15. 10.1146/annurev.bi.54.070185.001131 / Annu. Rev. Biochem. / Mechanisms and control of transcription initiation in prokaryotes by McClure (1985)
  16. 10.1006/jmbi.1996.0230 / J. Mol. Biol. / Transcription activation parameters at ara pBAD by Zhang (1996)
  17. 10.1074/jbc.M310471200 / J. Biol. Chem. / Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase by Skinner (2004)
  18. 10.1038/nrm1981 / Nat. Rev. Mol. Cell Biol. / Breaking barriers to transcription elongation by Saunders (2006)
  19. 10.1038/nature02191 / Nature / Backtracking by single RNA polymerase molecules observed at near base pair resolution by Shaevitz (2003)
  20. 10.1016/S0092-8674(03)00845-6 / Cell / Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking by Neuman (2003)
  21. 10.1016/j.cell.2006.04.032 / Cell / Sequence-resolved detection of pausing by single RNA polymerase molecules by Herbert (2006)
  22. 10.1073/pnas.142417799 / Proc. Natl. Acad. Sci. USA / Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase by Forde (2002)
  23. 10.1126/science.1127422 / Science / Transcript-assisted transcriptional proofreading by Zenkin (2006)
  24. 10.1016/j.cell.2004.07.021 / Cell / Regulation of RNA polymerase through the secondary channel by Nickels (2004)
  25. 10.1074/jbc.273.27.16843 / J. Biol. Chem. / Recognition of a human arrest site is conserved between RNA polymerase II and prokaryotic RNA polymerases by Mote (1998)
  26. 10.1006/jmbi.1996.0707 / J. Mol. Biol. / A model for the mechanism of polymerase translocation by Guajardo (1997)
  27. 10.1016/S0006-3495(98)77833-6 / Biophys. J. / Motion of RNA polymerase along DNA: a stochastic model by Julicher (1998)
  28. 10.1016/j.jmb.2004.08.107 / J. Mol. Biol. / Sequence-dependent kinetic model for transcription elongation by RNA polymerase by Bai (2004)
  29. 10.1073/pnas.0600508103 / Proc. Natl. Acad. Sci. USA / Thermodynamic and kinetic modeling of transcription pausing by Tadigotla (2006)
  30. 10.1371/journal.pbio.0040309 / PLOS Biol. / Stochastic mRNA synthesis in mammalian cells by Raj (2006)
  31. 10.1016/j.cub.2006.03.092 / Curr. Biol. / Transcriptional pulsing of a developmental gene by Chubb (2006)
  32. 10.1126/science.289.5479.619 / Science / A structural model of transcription elongation by Korzheva (2000)
  33. 10.1016/S0092-8674(00)80180-4 / Cell / The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase by Nudler (1997)
  34. 10.1073/pnas.94.5.1755 / Proc. Natl. Acad. Sci. USA / Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded by Komissarova (1997)
  35. {'key': '10.1529/biophysj.107.105767_bib35', 'first-page': '459', 'article-title': 'Transcript cleavage factor from', 'volume': '72', 'author': 'Borukhov', 'year': '1993', 'journal-title': 'E. coli. Cell'} / E. coli. Cell / Transcript cleavage factor from by Borukhov (1993)
  36. 10.1016/S0167-4781(02)00459-1 / Biochim. Biophys. Acta / Promoting elongation with transcript cleavage stimulatory factors by Fish (2002)
  37. {'year': '1992', 'series-title': 'Stochastic Processes in Physics and Chemistry', 'author': 'van Kampen', 'key': '10.1529/biophysj.107.105767_bib37'} / Stochastic Processes in Physics and Chemistry by van Kampen (1992)
  38. {'year': '2004', 'series-title': 'Handbook of Stochastic Methods for Physics, Chemistry, and the Natural Sciences', 'author': 'Gardiner', 'key': '10.1529/biophysj.107.105767_bib38'} / Handbook of Stochastic Methods for Physics, Chemistry, and the Natural Sciences by Gardiner (2004)
  39. {'year': '2001', 'series-title': 'A Guide to First-Passage Processes', 'author': 'Redner', 'key': '10.1529/biophysj.107.105767_bib39'} / A Guide to First-Passage Processes by Redner (2001)
  40. 10.1128/jb.173.20.6647-6649.1991 / J. Bacteriol. / rRNA transcription rate in Escherichia coli by Gotta (1991)
  41. 10.1103/PhysRevE.52.2912 / Phys. Rev. E / Statistical mechanics of supercoiled DNA by Marko (1995)
  42. 10.1103/PhysRevE.69.061907 / Phys. Rev. E / Statistical mechanics of double-helical polymers by Col (2004)
  43. 10.1007/BF01052811 / J. Stat. Phys. / Exact solution of the totally asymmetric simple exclusion process: shock profiles by Derrida (1993)
  44. 10.1103/PhysRevLett.74.208 / Phys. Rev. Lett. / Spontaneous symmetry breaking in a one-dimensional driven diffusive system by Evans (1995)
  45. 10.1016/0167-4781(95)00042-F / Biochim. Biophys. Acta / Guanosine tetraphosphate as a global regulator of bacterial RNA synthesis: a model involving RNA polymerase pausing and queuing by Bremer (1995)
  46. 10.1073/pnas.97.13.7090 / Proc. Natl. Acad. Sci. USA / Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals by Artsimovitch (2000)
  47. 10.1016/j.cell.2007.01.015 / Cell / The role of chromatin during transcription by Li (2007)
  48. 10.1016/j.molcel.2006.09.012 / Mol. Cell. / RSC Exploits histone acetylation to abrogate the nucleosomal block to RNA polymerase II elongation by Carey (2006)
  49. 10.1529/biophysj.106.086157 / Biophys. J. / Diffusion of transcription factors can drastically enhance the noise in gene expression by van Zon (2006)
  50. 10.1021/bi00368a013 / Biochemistry / An RNA polymerase mutant with reduced accuracy of chain elongation by Blank (1986)
  51. Reference deleted in proof.
  52. 10.1073/pnas.90.17.7923 / Proc. Natl. Acad. Sci. USA / In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes by Rasmussen (1993)
  53. 10.1016/j.molcel.2004.11.028 / Mol. Cell. / Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS by Adelman (2005)
  54. 10.1126/science.1065329 / Science / An extensive class of small RNAs in Caenorhabditis elegans complementarity to lin-14 by Lee (2001)
  55. 10.1126/science.1064921 / Science / Identification of novel genes coding for small expressed RNAs by Lagos-Quintana (2001)
  56. 10.1126/science.1065062 / Science / An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans by Lau (2001)
  57. 10.1038/nature05701 / Nature / Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner by Galburt (2007)
  58. {'year': '1973', 'series-title': 'Tables of Laplace Transforms', 'author': 'Oberhettinger', 'key': '10.1529/biophysj.107.105767_bib58'} / Tables of Laplace Transforms by Oberhettinger (1973)
  59. 10.1021/j100540a008 / J. Phys. Chem. / Exact stochastic simulation of coupled chemical reactions by Gillespie (1977)
  60. {'year': '1986', 'series-title': 'Monte Carlo Methods in Statistical Physics', 'author': 'Binder', 'key': '10.1529/biophysj.107.105767_bib60'} / Monte Carlo Methods in Statistical Physics by Binder (1986)
  61. 10.1016/S0021-9258(19)69683-3 / J. Biol. Chem. / A direct effect of guanosine tetraphosphate on pausing of Escherichia coli RNA polymerase during RNA chain elongation by Kingston (1981)
  62. 10.1126/science.270.5242.1653 / Science / Transcription against an applied force by Yin (1995)
  63. 10.1038/352444a0 / Nature / Transcription by single molecules of RNA polymerase observed by light microscopy by Schafer (1991)
Dates
Type When
Created 18 years ago (Aug. 24, 2007, 8:40 p.m.)
Deposited 1 year ago (Aug. 12, 2024, 6:26 a.m.)
Indexed 4 months ago (April 30, 2025, 3:30 a.m.)
Issued 17 years, 8 months ago (Jan. 1, 2008)
Published 17 years, 8 months ago (Jan. 1, 2008)
Published Print 17 years, 8 months ago (Jan. 1, 2008)
Funders 4
  1. Royal Society 10.13039/501100000288

    Region: Europe

    pri (Associations and societies (private and public))

    Labels1
    1. The Royal Society
  2. University of Leeds 10.13039/501100000777
  3. Medical Research Council 10.13039/501100000265

    Region: Europe

    gov (National government)

    Labels3
    1. Medical Research Council (United Kingdom)
    2. UK Medical Research Council
    3. MRC
    Awards1
    1. G0300556
  4. Engineering and Physical Sciences Research Council 10.13039/501100000266

    Region: Europe

    gov (National government)

    Labels4
    1. UKRI Engineering and Physical Sciences Research Council
    2. Engineering and Physical Sciences Research Council - UKRI
    3. Engineering & Physical Sciences Research Council
    4. EPSRC
    Awards2
    1. EP/C011953/1
    2. EP/D003105

@article{Voliotis_2008, title={Fluctuations, Pauses, and Backtracking in DNA Transcription}, volume={94}, ISSN={0006-3495}, url={http://dx.doi.org/10.1529/biophysj.107.105767}, DOI={10.1529/biophysj.107.105767}, number={2}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Voliotis, Margaritis and Cohen, Netta and Molina-París, Carmen and Liverpool, Tanniemola B.}, year={2008}, month=jan, pages={334–348} }