Molecular Mechanisms of Transcription through Single-Molecule Experiments

Transcription represents the first step in gene expression. It is therefore not surprising that transcription is a highly regulated process and its control is essential to understand the flow and processing of information required by the cell to maintain its homeostasis. During transcription, a DNA molecule is copied into RNA molecules that are then used to translate the genetic information into proteins; this logical pattern has been conserved throughout all three kingdoms of life, from Archaea to Eukarya, making it an essential and fundamental cellular process. Even though some viruses that encode their genome in an RNA molecule use it as a template to make mRNA, others synthesize an intermediate DNA molecule from the RNA, a process known as reverse transcription, from which regular transcription of viral genes can then proceed in the host cells.

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

[2]  Ilya J. Finkelstein,et al.  The promoter search mechanism of E. coli RNA polymerase is dominated by three–dimensional diffusion , 2012, Nature Structural &Molecular Biology.

[3]  Nancy R. Forde,et al.  Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[4]  J. Parrondo,et al.  RNA polymerase pushing. , 2011, Biophysical chemistry.

[5]  M. Hecker,et al.  LicT, a Bacillus subtilis transcriptional antiterminator protein of the BglG family , 1996, Journal of bacteriology.

[6]  J. Richardson.  Rho-dependent termination and ATPases in transcript termination. , 2002, Biochimica et biophysica acta.

[7]  M. Kashlev,et al.  Mechanism of sequence-specific pausing of bacterial RNA polymerase , 2009, Proceedings of the National Academy of Sciences.

[8]  Zachary F Burton,et al.  Translocation by multi-subunit RNA polymerases. , 2010, Biochimica et biophysica acta.

[9]  Elio A. Abbondanzieri,et al.  Ubiquitous Transcriptional Pausing Is Independent of RNA Polymerase Backtracking , 2003, Cell.

[10]  Steven M. Block,et al.  Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II , 2012, Proceedings of the National Academy of Sciences.

[11]  P. V. von Hippel,et al.  Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. , 1993, Science.

[12]  R. Ebright,et al.  Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. , 2006, Biophysical journal.

[13]  K. Murakami,et al.  Single-molecule imaging of RNA polymerase-DNA interactions in real time. , 1999, Biophysical journal.

[14]  Robert Landick,et al.  The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. , 2003, Molecular cell.

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

[16]  S. Borukhov,et al.  Transcript cleavage factors from E. coli , 1993, Cell.

[17]  A. Mehta,et al.  Single-molecule biomechanics with optical methods. , 1999, Science.

[18]  P K Hansma,et al.  Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. , 1999, Biophysical journal.

[19]  J. Gelles,et al.  Mechanism of Transcription Initiation at an Activator-Dependent Promoter Defined by Single-Molecule Observation , 2012, Cell.

[20]  J. Champoux.  DNA topoisomerases: structure, function, and mechanism. , 2001, Annual review of biochemistry.

[21]  Carlos Bustamante,et al.  Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner , 2007, Nature.

[22]  Michelle D. Wang,et al.  A single-molecule technique to study sequence-dependent transcription pausing. , 2004, Biophysical journal.

[23]  Michelle D. Wang,et al.  Transcription Under Torsion , 2013, Science.

[24]  R E Glass,et al.  Visualization of single molecules of RNA polymerase sliding along DNA. , 1993, Science.

[25]  G. Felsenfeld,et al.  A histone octamer can step around a transcribing polymerase without leaving the template , 1994, Cell.

[26]  M. Kashlev,et al.  RNA Polymerase Switches between Inactivated and Activated States By Translocating Back and Forth along the DNA and the RNA* , 1997, The Journal of Biological Chemistry.

[27]  Kirsten L. Frieda,et al.  Direct Observation of Cotranscriptional Folding in an Adenine Riboswitch , 2012, Science.

[28]  R. Reeder,et al.  Transcription termination of RNA polymerase I due to a T-rich element interacting with Reb1p. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[29]  C. Bustamante,et al.  Nucleosomal Elements that Control the Topography of the Barrier to Transcription , 2012, Cell.

[30]  Yuan He,et al.  Structural visualization of key steps in human transcription initiation , 2013, Nature.

[31]  K. Sakata-Sogawa,et al.  RNA polymerase can track a DNA groove during promoter search. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Ignacio Izeddin,et al.  Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells , 2013, Science.

[33]  Vasily M Studitsky,et al.  Nature of the nucleosomal barrier to RNA polymerase II. , 2005, Molecular cell.

[34]  M. Kashlev,et al.  Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[35]  D. Crothers,et al.  A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lac UV5 promoter. , 1987, Journal of molecular biology.

[36]  Steven M. Block,et al.  Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination , 2008, Cell.

[37]  C. Burns,et al.  Combinatorial effects of NusA and NusG on transcription elongation and Rho-dependent termination in Escherichia coli. , 1998, Journal of molecular biology.

[38]  S. Hahn,et al.  The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex , 2007, Nature Structural &Molecular Biology.

[39]  G. Felsenfeld,et al.  A nucleosome core is transferred out of the path of a transcribing polymerase , 1992, Cell.

[40]  M. Shin,et al.  Fast microscopical dissection of action scenes played by Escherichia coli RNA polymerase , 2012, FEBS letters.

[41]  A. Riggs,et al.  The lac repressor-operator interaction. 3. Kinetic studies. , 1970, Journal of molecular biology.

[42]  R. Ebright,et al.  Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  N. Proudfoot,et al.  Disengaging polymerase: Terminating RNA polymerase II transcription in budding yeast☆ , 2013, Biochimica et biophysica acta.

[44]  J. Gelles,et al.  RNA polymerase approaches its promoter without long-range sliding along DNA , 2013, Proceedings of the National Academy of Sciences.

[45]  R. Landick,et al.  Allosteric Control of RNA Polymerase by a Site That Contacts Nascent RNA Hairpins , 2001, Science.

[46]  Michael Levitt,et al.  Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex , 2013, Science.

[47]  D. Luse,et al.  Efficient and Rapid Nucleosome Traversal by RNA Polymerase II Depends on a Combination of Transcript Elongation Factors* , 2010, The Journal of Biological Chemistry.

[48]  Robert Landick,et al.  A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. , 2007, Molecular cell.

[49]  Shimon Weiss,et al.  Opening and Closing of the Bacterial RNA Polymerase Clamp , 2012, Science.

[50]  Steven M. Block,et al.  Sequence-Resolved Detection of Pausing by Single RNA Polymerase Molecules , 2006, Cell.

[51]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[52]  Shimon Weiss,et al.  Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism , 2006, Science.

[53]  E. Siggia,et al.  Entropic elasticity of lambda-phage DNA. , 1994, Science.

[54]  J. Richardson.  Activation of rho protein ATPase requires simultaneous interaction at two kinds of nucleic acid-binding sites. , 1982, The Journal of biological chemistry.

[55]  D. Kim,et al.  The Kinetic Pathway of RNA Binding to the Escherichia coli Transcription Termination Factor Rho* , 2001, The Journal of Biological Chemistry.

[56]  R. Burgess,et al.  Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-lambda PR promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening. , 1985, Journal of molecular biology.

[57]  S. Block,et al.  Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA. , 2011, Molecular cell.

[58]  J. Berger,et al.  Structure of the Rho Transcription Terminator Mechanism of mRNA Recognition and Helicase Loading , 2003, Cell.

[59]  Anirvan M. Sengupta,et al.  Thermodynamic and kinetic modeling of transcriptional pausing. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Joshua W. Shaevitz,et al.  Backtracking by single RNA polymerase molecules observed at near-base-pair resolution , 2003, Nature.

[61]  H. Blöcker,et al.  Predicting DNA duplex stability from the base sequence. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Michelle D. Wang,et al.  Sequence-dependent kinetic model for transcription elongation by RNA polymerase. , 2004, Journal of molecular biology.

[63]  T. Laurence,et al.  Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis. , 2005, Molecular cell.

[64]  Michelle D. Wang,et al.  Force and velocity measured for single molecules of RNA polymerase. , 1998, Science.

[65]  L. Reitzer,et al.  Metabolic Context and Possible Physiological Themes of ς54-Dependent Genes in Escherichia coli , 2001, Microbiology and Molecular Biology Reviews.

[66]  P. Cramer,et al.  Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution , 2001, Science.

[67]  R. Ebright,et al.  Upstream promoter sequences and αCTD mediate stable DNA wrapping within the RNA polymerase–promoter open complex , 2007, EMBO reports.

[68]  R. Tjian,et al.  Transcription initiation by human RNA polymerase II visualized at single-molecule resolution. , 2012, Genes & development.

[69]  C. Bustamante,et al.  Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. , 2000, Science.

[70]  E. Geiduschek,et al.  Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. , 1997, Science.

[71]  C. Bustamante,et al.  The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes , 2011, Nature Structural &Molecular Biology.

[72]  J. Wang,et al.  Supercoiling of the DNA template during transcription. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[73]  A. Weixlbaumer,et al.  Structural Basis of Transcriptional Pausing in Bacteria , 2013, Cell.

[74]  S. Gopinath,et al.  Insights into anti-termination regulation of the hut operon in Bacillus subtilis: importance of the dual RNA-binding surfaces of HutP , 2008, Nucleic Acids Research.

[75]  C. Bustamante,et al.  Facilitated Target Location on DNA by IndividualEscherichia coli RNA Polymerase Molecules Observed with the Scanning Force Microscope Operating in Liquid* , 1999, The Journal of Biological Chemistry.

[76]  C. Bustamante,et al.  Wrapping of DNA around the E.coli RNA polymerase open promoter complex , 1999, The EMBO journal.

[77]  S. Block,et al.  Binding and translocation of termination factor rho studied at the single-molecule level. , 2012, Journal of molecular biology.

[78]  S. Block,et al.  E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase. , 2010, Journal of molecular biology.

[79]  Jens Michaelis,et al.  Single-molecule tracking of mRNA exiting from RNA polymerase II , 2008, Proceedings of the National Academy of Sciences.

[80]  Steven Hahn,et al.  A transcription reinitiation intermediate that is stabilized by activator , 2000, Nature.

[81]  S. Hahn,et al.  Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex , 2010, The EMBO journal.

[82]  Michelle D. Wang,et al.  Synergistic action of RNA polymerases in overcoming the nucleosomal barrier , 2010, Nature Structural &Molecular Biology.

[83]  P. Dehaseth,et al.  Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. , 2011, Journal of molecular biology.

[84]  S. Hahn,et al.  Architecture of the Yeast RNA Polymerase II Open Complex and Regulation of Activity by TFIIF , 2011, Molecular and Cellular Biology.

[85]  K. Agarwal,et al.  Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[86]  C. Bustamante,et al.  Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism , 2013, eLife.

[87]  P. V. von Hippel,et al.  Facilitated Target Location in Biological Systems* , 2022 .

[88]  W. Greenleaf,et al.  Direct observation of base-pair stepping by RNA polymerase , 2005, Nature.

[89]  Martin Depken,et al.  The origin of short transcriptional pauses. , 2009, Biophysical journal.

[90]  Scott Forth,et al.  Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection , 2007, Nature Methods.

[91]  Jens Michaelis,et al.  Dynamic architecture of a minimal RNA polymerase II open promoter complex. , 2012, Molecular cell.

[92]  S. Hahn,et al.  Mapping the Location of TFIIB within the RNA Polymerase II Transcription Preinitiation Complex A Model for the Structure of the PIC , 2004, Cell.

[93]  E. Nudler,et al.  Isolation and Characterization of σ70-Retaining Transcription Elongation Complexes from Escherichia coli , 2001, Cell.

[94]  Carlos Bustamante,et al.  Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II , 2009, Science.

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

[96]  D. K. Hawley,et al.  Transcriptional Fidelity and Proofreading by RNA Polymerase II , 1998, Cell.

[97]  Terence R. Strick,et al.  Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching , 2006, Science.

[98]  P. Cramer,et al.  Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. , 2009, Molecular cell.

[99]  W. Greenleaf,et al.  Single-molecule studies of RNA polymerase: motoring along. , 2008, Annual review of biochemistry.

[100]  V. Studitsky,et al.  RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones , 2010, Proceedings of the National Academy of Sciences.

[101]  Michael D. Stone,et al.  Structural transitions and elasticity from torque measurements on DNA , 2003, Nature.

[102]  D. Lindstrom,et al.  Transcript elongation on a nucleoprotein template. , 2002, Biochimica et biophysica acta.

[103]  S. Hahn,et al.  A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex , 2006, Nature Structural &Molecular Biology.

[104]  R. Sousa,et al.  A model for the mechanism of polymerase translocation. , 1997, Journal of molecular biology.

[105]  C. Gross,et al.  Multiple sigma subunits and the partitioning of bacterial transcription space. , 2003, Annual review of microbiology.

[106]  E. Margeat,et al.  Competitive folding of anti-terminator/terminator hairpins monitored by single molecule FRET , 2013, Nucleic acids research.

[107]  A. Serganov,et al.  Metabolite recognition principles and molecular mechanisms underlying riboswitch function. , 2012, Annual review of biophysics.

[108]  Bradley M. Zamft,et al.  Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases , 2012, Proceedings of the National Academy of Sciences.

[109]  K. Murakami,et al.  Bacterial RNA polymerases: the wholo story. , 2003, Current opinion in structural biology.

[110]  R. Kornberg,et al.  Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome , 1999, Cell.

[111]  Steven M. Block,et al.  Transcription Against an Applied Force , 1995, Science.

[112]  A. Németh,et al.  RNA polymerase I termination: Where is the end? , 2013, Biochimica et biophysica acta.

[113]  Richard J Maraia,et al.  Transcription termination by the eukaryotic RNA polymerase III. , 2013, Biochimica et biophysica acta.

[114]  R. Landick,et al.  Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[115]  S. Mizutani,et al.  Viral RNA-dependent DNA Polymerase: RNA-dependent DNA Polymerase in Virions of Rous Sarcoma Virus , 1970, Nature.

[116]  R. Roeder,et al.  The role of general initiation factors in transcription by RNA polymerase II. , 1996, Trends in biochemical sciences.

[117]  R. Landick,et al.  Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase , 2007, Proceedings of the National Academy of Sciences.

[118]  J. Stülke,et al.  Specific interaction of the RNA-binding domain of the bacillus subtilis transcriptional antiterminator GlcT with its RNA target, RAT. , 1999, Journal of molecular biology.