M. Kashlev

发表

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

R. Sandberg, Shalini Oberdoerffer, S. Shukla, 2011, Nature.

Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs.

Wade W Grabow, Wade W. Grabow, L. Jaeger, 2012, Nano letters.

In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles

B. Shapiro, E. Bindewald, M. Kashlev, 2014, Accounts of chemical research.

Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage.

D. Gotte, J. Strathern, P. Cramer, 2012, Molecules and Cells.

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

C. Bustamante, Toyotaka Ishibashi, M. Kashlev, 2013, eLife.

Escherichia coli σ38 promoters use two UP elements instead of a −35 element: resolution of a paradox and discovery that σ38 transcribes ribosomal promoters

T. D. Schneider, M. Kashlev, D. Jin, 2020, bioRxiv.

Escherichia coli RNA polymerase activity observed using atomic force microscopy.

P K Hansma, C. Bustamante, H. Hansma, 1997, Biochemistry.

Topology of the RNA polymerase active center probed by chimeric rifampicin-nucleotide compounds.

K. Severinov, M. Kashlev, A. Goldfarb, 1994, Proceedings of the National Academy of Sciences of the United States of America.

Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner

Carlos Bustamante, Stephan W. Grill, Jason Choy, 2007, Nature.

Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities

B. Shapiro, E. Bindewald, M. Kashlev, 2013, Nucleic acids research.

Coupling between transcription termination and RNA polymerase inchworming

E. Nudler, M. Kashlev, A. Goldfarb, 1995, Cell.

Sensitivity of Mitochondrial Transcription and Resistance of RNA Polymerase II Dependent Nuclear Transcription to Antiviral Ribonucleosides

J. Arnold, C. Cameron, A. Gnatt, 2012, PLoS pathogens.

Heat shock response in Escherichia coli promotes assembly of plasmid encoded RNA polymerase β-subunit into RNA polymerase

M. Kashlev, V. Nikiforov, A. Gragerov, 1989, Molecular and General Genetics MGG.

A Cre Transcription Fidelity Reporter Identifies GreA as a Major RNA Proofreading Factor in Escherichia coli

D. Court, D. Gotte, J. Strathern, 2017, Genetics.

A Genetic Assay for Transcription Errors Reveals Multilayer Control of RNA Polymerase II Fidelity

D. Gotte, B. Shafer, J. Strathern, 2014, PLoS genetics.

Histidine-tagged RNA polymerase: dissection of the transcription cycle using immobilized enzyme.

K. Severinov, M. Kashlev, A. Goldfarb, 1993, Gene.

Bacteriophage T4 Alc protein: A transcription termination factor sensing local modification of DNA

E. Nudler, M. Kashlev, E. Kutter, 1993, Cell.

Discontinuous mechanism of transcription elongation.

M. Kashlev, A. Goldfarb, E. Nudler, 1994, Science.

Transcription elongation

T. Oshima, M. Imashimizu, M. Kashlev, 2014, Transcription.

RNA Polymerases and Transcription

M. Kashlev, M. Kireeva, Z. Burton, 2018 .

Production and characterization of a highly pure RNA polymerase holoenzyme from Mycobacterium tuberculosis.

C. Bustamante, M. Kashlev, M. Kireeva, 2017, Protein expression and purification.

Cotranscriptional Production of Chemically Modified RNA Nanoparticles.

B. Shapiro, M. Kashlev, K. Afonin, 2017, Methods in molecular biology.

Strategies and methods of cross-linking of RNA polymerase active center.

V. Markovtsov, K. Severinov, M. Kashlev, 2003, Methods in enzymology.

RNA–DNA and DNA–DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate

M. Kashlev, M. Kireeva, L. Lubkowska, 2018, Nucleic acids research.

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase

Yun-Xing Wang, X. Ji, M. Kashlev, 2015, The Journal of Biological Chemistry.

Isolation and Characterization of RNA Polymerase rpoB Mutations That Alter Transcription Slippage during Elongation in Escherichia coli*

D. Court, J. Strathern, M. Kashlev, 2012, The Journal of Biological Chemistry.

A beta subunit mutation disrupting the catalytic function of Escherichia coli RNA polymerase.

M. Kashlev, S. Borukhov, J. Lee, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Transcription through the nucleosome by mRNA-producing RNA polymerases.

M. Kashlev, V. Studitsky, W. Walter, 2004, Methods in enzymology.

Mapping of Catalytic Residues in the RNA Polymerase Active Center

V. Markovtsov, M. Kashlev, H. Heumann, 1996, Science.

RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression.

M. Kashlev, M. Kireeva, Z. Burton, 2013, Chemical reviews.

Nature of the nucleosomal barrier to RNA polymerase II.

Vasily M Studitsky, M. Kashlev, V. Studitsky, 2005, Molecular cell.

The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex*

M. Kashlev, D. Waugh, M. Kireeva, 2000, The Journal of Biological Chemistry.

The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.

R. Cukier, E. Nudler, M. Kashlev, 2013, Biochimica et biophysica acta.

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

Benoit Coulombe, Robert I Cukier, Zachary F Burton, 2012, BMC biophysics.

Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.

Michael Feig, Michael Hampsey, Benoit Coulombe, 2010, Biochimica et biophysica acta.

Translocation by multi-subunit RNA polymerases.

Zachary F Burton, M. Kashlev, M. Kireeva, 2010, Biochimica et biophysica acta.

Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II.

B. Coulombe, M. Kashlev, J. Archambault, 2010, Protein expression and purification.

Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase.

M. Kashlev, Y. Nedialkov, Chunfen Zhang, 2009, Methods.

Transcription elongation: Heterogeneous tracking of RNA polymerase and its biological implications.

T. Oshima, M. Imashimizu, M. Kashlev, 2014, Transcription.

Mechanism of sequence-specific pausing of bacterial RNA polymerase

M. Kashlev, M. Kireeva, 2009, Proceedings of the National Academy of Sciences.

Rpb9 Subunit Controls Transcription Fidelity by Delaying NTP Sequestration in RNA Polymerase II*♦

J. Strathern, M. Kashlev, Y. Nedialkov, 2009, The Journal of Biological Chemistry.

Mutations in the Saccharomyces cerevisiae RPB1 Gene Conferring Hypersensitivity to 6-Azauracil

B. Shafer, J. Strathern, M. Kashlev, 2006, Genetics.

Mutations in the Saccharomyces cerevisiae RPB 1 Gene Conferring Hypersensitivity to 6 -

B. Shafer, M. Kashlev, M. Kireeva, 2006 .

Chromatin remodeling by RNA polymerases.

G. Felsenfeld, M. Kashlev, V. Studitsky, 2004, Trends in biochemical sciences.

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II

Wei Wang, Dong Wang, M. Kashlev, 2018, Proceedings of the National Academy of Sciences.

Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions

A. Gnatt, Dong Wang, M. Kashlev, 2015, Proceedings of the National Academy of Sciences.

Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation.

J. Strathern, M. Kashlev, Y. Nedialkov, 2008, Molecular cell.

Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity.

M. Kashlev, M. Kireeva, N. Komissarova, 2000, Journal of molecular biology.

Mapping of trypsin cleavage and antibody-binding sites and delineation of a dispensable domain in the beta subunit of Escherichia coli RNA polymerase.

K. Severinov, M. Kashlev, S. Borukhov, 1991, The Journal of biological chemistry.

Bacterial Polymerase and Yeast Polymerase II Use Similar Mechanisms for Transcription through Nucleosomes*

M. Kashlev, V. Studitsky, M. Kireeva, 2003, Journal of Biological Chemistry.

Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae.

M. Kashlev, M. Kireeva, L. Lubkowska, 2003, Methods in enzymology.

Functional topography of nascent RNA in elongation intermediates of RNA polymerase.

M. Kashlev, N. Komissarova, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Crucial role of the RNA:DNA hybrid in the processivity of transcription.

M. Kashlev, N. Komissarova, I. Sidorenkov, 1998, Molecules and Cells.

RNA Polymerase Switches between Inactivated and Activated States By Translocating Back and Forth along the DNA and the RNA*

M. Kashlev, N. Komissarova, 1997, The Journal of Biological Chemistry.

Interaction of RNA Polymerase II Fork Loop 2 with Downstream Non-template DNA Regulates Transcription Elongation*

B. Coulombe, M. Kashlev, M. Kireeva, 2011, The Journal of Biological Chemistry.

Unveiling translocation intermediates of RNA polymerase

M. Imashimizu, M. Kashlev, 2014, Proceedings of the National Academy of Sciences.

Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics

C. Bustamante, Toyotaka Ishibashi, M. Kashlev, 2014, Proceedings of the National Academy of Sciences.

Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded.

M. Kashlev, N. Komissarova, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II.

D. Gotte, J. Strathern, M. Imashimizu, 2013, Journal of molecular biology.

The Fidelity of Transcription

D. Gotte, B. Shafer, J. Strathern, 2012, The Journal of Biological Chemistry.

Direct assessment of transcription fidelity by high-resolution RNA sequencing

T. Oshima, M. Imashimizu, M. Kashlev, 2013, Nucleic acids research.

Erratum to: Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo

D. Court, T. Oshima, M. Imashimizu, 2015, Genome Biology.

Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo

D. Court, T. Oshima, M. Imashimizu, 2015, Genome Biology.

Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators

J. F. Atkins, P. Baranov, Virag Sharma, 2015, Proceedings of the National Academy of Sciences.

Coliphage HK022 Nun protein inhibits RNA polymerase translocation

M. Kashlev, M. Gottesman, M. Kireeva, 2014, Proceedings of the National Academy of Sciences.

Bacteriophage λ N protein inhibits transcription slippage by Escherichia coli RNA polymerase

D. Court, M. Kashlev, D. Jin, 2014, Nucleic acids research.

DNA bending in transcription initiation.

H. Halvorson, M. Kashlev, Vladimir Tchernaenko, 2008, Biochemistry.

A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc.

K. Severinov, M. Kashlev, E. Kutter, 1994, The Journal of biological chemistry.

Isolation and characterization of transcription fidelity mutants.

D. Court, J. Strathern, M. Kashlev, 2012, Biochimica et biophysica acta.

DNA sequences in gal operon override transcription elongation blocks.

M. Kashlev, S. Adhya, D. Lewis, 2008, Journal of molecular biology.

The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase.

M. Imashimizu, M. Kashlev, N. Shimamoto, 2019, Journal of molecular biology.

Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination.

M. Kashlev, M. Kireeva, J. Becker, 2002, Molecular cell.

Transcription Termination: Primary Intermediates and Secondary Adducts*

M. Kashlev, N. Komissarova, 2002, The Journal of Biological Chemistry.

Dissection of the beta subunit in the Escherichia coli RNA polymerase into domains by proteolytic cleavage.

K. Severinov, M. Kashlev, S. Borukhov, 1992, The Journal of biological chemistry.

Mapping of the priming substrate contacts in the active center of Escherichia coli RNA polymerase.

M. Kashlev, J. Lee, A. Goldfarb, 1991, The Journal of biological chemistry.

Engineering of elongation complexes of bacterial and yeast RNA polymerases.

M. Kashlev, M. Kireeva, J. Becker, 2003, Methods in enzymology.

The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes

C. Bustamante, Lacramioara Bintu, M. Kashlev, 2011, Nature Structural &Molecular Biology.

Single-molecule experiments have shed new light on the mechanisms responsible for the movement of RNA polymerase along DNA during transcription.

Robert A. Forties, Michelle D. Wang, Toyotaka Ishibashi, 2013 .

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

Michelle D. Wang, Lu Bai, R. M. Fulbright, 2010, Nature Structural &Molecular Biology.

Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria

M. Kashlev, P. FitzGerald, A. Yakhnin, 2020, Nature Communications.

Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase.

E. Nudler, K. Severinov, M. Kashlev, 1996, Methods in enzymology.

Transcriptome-Wide Effects of NusA on RNA Polymerase Pausing in Bacillus subtilis

M. Kashlev, P. Babitzke, A. Yakhnin, 2022, Journal of bacteriology.

NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA

M. Kashlev, P. Babitzke, A. Yakhnin, 2021, eLife.

NusG-dependent RNA polymerase pausing is a frequent function of this universally conserved transcription elongation factor

M. Kashlev, P. Babitzke, A. Yakhnin, 2020, Critical reviews in biochemistry and molecular biology.

NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome

M. Kashlev, C. Mcintosh, P. FitzGerald, 2020, Proceedings of the National Academy of Sciences.

NusG-Dependent RNA Polymerase Pausing and Tylosin-Dependent Ribosome Stalling Are Required for Tylosin Resistance by Inducing 23S rRNA Methylation in Bacillus subtilis

M. Kashlev, P. Babitzke, A. Yakhnin, 2019, mBio.

T7 replisome directly overcomes DNA damage

Michelle D. Wang, M. Kashlev, Smita S. Patel, 2015, Nature Communications.

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

Carlos Bustamante, C. Bustamante, Lacramioara Bintu, 2009, Science.

Assay of the fate of the nucleosome during transcription by RNA polymerase II.

M. Kashlev, V. Studitsky, M. Kireeva, 2003, Methods in enzymology.

Effects of Friedreich's ataxia (GAA)n·(TTC)n repeats on RNA synthesis and stability.

S. Mirkin, M. Kashlev, V. Petrovic, 2007, Nucleic acids research.

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

C. Bustamante, Lacramioara Bintu, Toyotaka Ishibashi, 2012, Cell.

Comprehensive transcription terminator atlas for Bacillus subtilis

K. Murakami, M. Kashlev, P. Babitzke, 2022, Nature Microbiology.

NusG is an intrinsic transcription termination factor that stimulates motility and coordinates global gene expression with NusA

M. Kashlev, P. Babitzke, A. Yakhnin, 2020, bioRxiv.

Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription.

M. Kashlev, V. Studitsky, M. Kireeva, 2002, Molecular cell.

Complete dissection of transcription elongation reveals slow translocation of Pol II in a linear ratchet mechanism

C. Bustamante, Toyotaka Ishibashi, M. Kashlev, 2014 .

Molecular cloning and characterization of Borrelia burgdorferi rpoB.

I. Schwartz, M. Kashlev, M. Alekshun, 1997, Gene.

Nucleosome Remodeling Induced by RNA Polymerase II : Loss of the H 2 A / H 2 B Dimer during Transcription date passage of RNAP ?

M. Kashlev, V. Studitsky, M. Kireeva, 2002 .

The fidelity of transcription in human cells

J. Strathern, B. Benayoun, Xinmin Zhang, 2022, bioRxiv.

Active center rearrangement in RNA polymerase initiation complex.

M. Kashlev, A. Goldfarb, M. Grachev, 1993, The Journal of biological chemistry.

Oriented, active Escherichia coli RNA polymerase: an atomic force microscope study.

P K Hansma, P. Hansma, E. Kool, 1999, Biophysical journal.

Blocking of the initiation-to-elongation transition by a transdominant RNA polymerase mutation.

M. Kashlev, J. Lee, A. Goldfarb, 1990, Science.

Protein aggregation and inclusion body formation in Escherichia coli rpoH mutant defective in heat shock protein induction

M. Kashlev, V. Nikiforov, A. Gragerov, 1991, FEBS letters.

Motion and enzymatic degradation of DNA in the atomic force microscope.

H. Hansma, P. Hansma, M. Kashlev, 1994, Biophysical journal.

Iodine-125 radioprobing of E. coli RNA polymerase transcription elongation complexes.

V. Zhurkin, M. Kashlev, I. Panyutin, 2003, Methods in enzymology.

Erratum to: Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo

D. Court, T. Oshima, M. Imashimizu, 2015, Genome Biology.

Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo

D. Court, T. Oshima, M. Imashimizu, 2015, Genome Biology.

Translocation by multi-subunit RNA polymerases.

M. Kashlev, M. Kireeva, Z. Burton, 2010, Biochimica et biophysica acta.

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

C. Bustamante, Toyotaka Ishibashi, M. Kashlev, 2013, eLife.

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II

Wei Wang, Dong Wang, M. Kashlev, 2018, Proceedings of the National Academy of Sciences.

Transcription elongation

T. Oshima, M. Kashlev, N. Shimamoto, 2014, Transcription.

Assembly of functional Escherichia coli RNA polymerase containing beta subunit fragments.

K. Severinov, S. Darst, M. Kashlev, 1995, Proceedings of the National Academy of Sciences of the United States of America.