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Our Science – Kashlev Website

Mikhail Kashlev, Ph.D.

Selected Publications

1)  Vitiello CL, Kireeva ML, Lubkowska L, Kashlev M, Gottesman M.
Coliphage HK022 Nun protein inhibits RNA polymerase translocation.
Proc. Natl. Acad. Sci. U.S.A. 2014.
[Journal]
2)  Imashimizu M, Kashlev M.
Unveiling translocation intermediates of RNA polymerase.
Proc. Natl. Acad. Sci. U.S.A. 2014.
[Journal]
3)  Parks AR, Court C, Lubkowska L, Jin DJ, Kashlev M, Court DL.
Bacteriophage lambda N protein inhibits transcription slippage by Escherichia coli RNA polymerase.
Nucleic Acids Res. [Epub ahead of print], 2014.
[Journal]
4)  Afonin KA, Desai R, Viard M, Kireeva ML, Bindewald E, Case CL, Maciag AE, Kasprzak WK, Kim T, Sappe A, Stepler M, Kewalramani VN, Kashlev M, Blumenthal R, Shapiro BA.
Co-transcriptional production of RNA-DNA hybrids for simultaneous release of multiple split functionalities.
Nucleic Acids Res. 42: 2085-97, 2014.
[Journal]
5)  Afonin KA, Kasprzak WK, Bindewald E, Kireeva M, Viard M, Kashlev M, Shapiro BA.
In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles.
Acc. Chem. Res. [Epub ahead of print], 2014.
[Journal]
6)  Imashimizu M, Shimamoto N, Oshima T, Kashlev M.
Transcription elongation: Heterogeneous tracking of RNA polymerase and its biological implications.
Transcription. 5, 2014.
[Journal]
7)  Ishibashi T, Dangkulwanich M, Coello Y, Lionberger TA, Lubkowska L, Ponticelli AS, Kashlev M, Bustamante C.
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics.
Proc. Natl. Acad. Sci. U.S.A. 111: 3419-24, 2014.
[Journal]
8)  Dangkulwanich M, Ishibashi T, Liu S, Kireeva ML, Lubkowska L, Kashlev M, Bustamante CJ.
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism.
Elife. 2: e00971, 2013.
[Journal]
9)  Imashimizu M, Oshima T, Lubkowska L, Kashlev M.
Direct assessment of transcription fidelity by high-resolution RNA sequencing.
Nucleic Acids Res. 41: 9090-104, 2013.
[Journal]
10)  Kireeva ML, Kashlev M, Burton ZF.
RNA Polymerase Structure, Function, Regulation, Dynamics, Fidelity, and Roles in GENE EXPRESSION.
Chem. Rev. 113: 8325-30, 2013.
[Journal]
11)  Strathern J, Malagon F, Irvin J, Gotte D, Shafer B, Kireeva ML, Lubkowska L, Jin DJ, Kashlev M.
The fidelity of transcription: RPB1 (RPOo21) mutations that increase transcriptional slippage in S. cerevisiae.
J. Biol. Chem. 288: 2689-99, 2013.
[Journal]
12)  Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, Cukier RI, Nudler E, Burton ZF.
The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.
Biochim. Biophys. Acta. 1829: 187-98, 2013.
[Journal]
13)  Afonin KA, Kireeva M, Grabow WW, Kashlev M, Jaeger L, Shapiro BA.
Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs.
Nano Lett. 12: 5192-5, 2012.
[Journal]
14)  Imashimizu M, Kireeva ML, Lubkowska L, Gotte D, Parks AR, Strathern JN, Kashlev M.
Intrinsic Translocation Barrier as an Initial Step in Pausing by RNA Polymerase II.
J. Mol. Biol. 425: 697-712, 2012.
[Journal]
15)  Zhou YN, Lubkowska L, Hui M, Court C, Chen S, Court DL, Strathern J, Jin DJ, Kashlev M.
Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in E. coli.
J. Biol. Chem. 288: 2700-10, 2012.
[Journal]
16)  Strathern JN, Jin DJ, Court DL, Kashlev M.
Isolation and characterization of transcription fidelity mutants.
Biochim. Biophys. Acta. 1819: 694-9, 2012.
[Journal]
17)  Walmacq C, Cheung AC, Kireeva ML, Lubkowska L, Ye C, Gotte D, Strathern JN, Carell T, Cramer P, Kashlev M.
Mechanism of Translesion Transcription by RNA Polymerase II and Its Role in Cellular Resistance to DNA Damage.
Mol Cell. 46: 18-29, 2012.
[Journal]
18)  Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, Kashlev M, Burton ZF.
Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.
BMC Biophys. 5: 11, 2012.
[Journal]
19)  Bintu L, Ishibashi T, Dangkulwanich M, Wu YY, Lubkowska L, Kashlev M, Bustamante C.
Nucleosomal Elements that Control the Topography of the Barrier to Transcription.
Cell. 151: 738-49, 2012.
[Journal]
20)  Arnold JJ, Sharma SD, Feng JY, Ray AS, Smidansky ED, Kireeva ML, Cho A, Perry J, Vela JE, Park Y, Xu Y, Tian Y, Babusis D, Barauskus O, Peterson BR, Gnatt A, Kashlev M, Zhong W, Cameron CE.
Sensitivity of Mitochondrial Transcription and Resistance of RNA Polymerase II Dependent Nuclear Transcription to Antiviral Ribonucleosides.
PLoS Pathog. 8: e1003030, 2012.
[Journal]
21)  Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S.
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Nature. 479: 74-9, 2011.
[Journal]
22)  Kireeva ML, Domecq C, Coulombe B, Burton ZF, Kashlev M.
Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.
J Biol Chem. [Epub ahead of prinit], 2011.
[Journal]
23)  Bintu L, Kopaczynska M, Hodges C, Lubkowska L, Kashlev M, Bustamante C.
The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes.
Nat Struct Mol Biol. 18: 1394-99, 2011.
Full Text Article. [Journal]
24)  Seibold SA, Singh BN, Zhang C, Kireeva M, Domecq C, Bouchard A, Nazione AM, Feig M, Cukier RI, Coulombe B, Kashlev M, Hampsey M, Burton ZF.
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.
Biochim Biophys Acta. [Epub ahead of print], 2010.
[Journal]
25)  Jin J, Bai L, Johnson DS, Fulbright RM, Kireeva ML, Kashlev M, Wang MD.
Synergistic action of RNA polymerases in overcoming the nucleosomal barrier.
Nat Struct Mol Biol. [Epub ahead of print], 2010.
[Journal]
26)  Kireeva M, Kashlev M, Burton ZF.
Translocation by multi-subunit RNA polymerases.
Biochim Biophys Acta. [Epub ahead of print], 2010.
[Journal]
27)  Kireeva ML, Kashlev M.
Mechanism of sequence-specific pausing of bacterial RNA polymerase.
Proc. Natl. Acad. Sci. U.S.A. [Epub ahead of print], 2009.
[Journal]
28)  Kireeva M, Nedialkov YA, Gong XQ, Zhang C, Xiong Y, Moon W, Burton ZF, Kashlev M.
Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase.
Methods. [Epub ahead of print], 2009.
[Journal]
29)  Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C.
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.
Science. 325: 626-8, 2009.
[Journal]
30)  Walmacq C, Kireeva ML, Irvin J, Nedialkov Y, Lubkowska L, Malagon F, Strathern JN, Kashlev M.
RPB9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II.
J. Biol. Chem. [Epub ahead of print], 2009.
[Journal]
31)  Domecq C, Kireeva M, Archambault J, Kashlev M, Coulombe B, Burton ZF.
Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II.
Protein Expr. Purif. [Epub ahead of print], 2009.
[Journal]
32)  Tchernaenko V, Radlinska M, Lubkowska L, Halvorson HR, Kashlev M, Lutter LC.
DNA Bending in Transcription Initiation.
Biochemistry. [Epub ahead of print], 2008.
[Journal]
33)  Tchernaenko V, Halvorson HR, Kashlev M, Lutter LC.
DNA Bubble Formation in Transcription Initiation.
Biochemistry. [Epub ahead of print], 2008.
[Journal]
34)  Lewis DE, Komissarova N, Le P, Kashlev M, Adhya S.
DNA sequences in gal operon override transcription elongation blocks.
J. Mol. Biol. 382: 843-58, 2008.
[Journal]
35)  Kireeva ML, Nedialkov YA, Cremona GH, Purtov YA, Lubkowska L, Malagon F, Burton ZF, Strathern JN, Kashlev M.
Transient reversal of RNA Polymerase II active site closing controls fidelity of transcription elongation.
Mol. Cell. 30: 557-66, 2008.
[Journal]
36)  Galburt EA, Grill SW, Wiedmann A, Lubkowska L, Choy J, Nogales E, Kashlev M, Bustamante C.
Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner.
Nature. 446: 820-823, 2007.
[Journal]
37)  Krasilnikova MM, Kireeva ML, Petrovic V, Knijnikova N, Kashlev M, Mirkin SM.
Effects of Friedreich's ataxia (GAA)n*(TTC)n repeats on RNA synthesis and stability.
Nucleic Acids Res. 35: 1075-84, 2007.
[Journal]
38)  Malagon F, Kireeva ML, Shafer BK, Lubkowska L, Kashlev M, Strathern JN.
Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil.
Genetics. 172: 2201-9, 2006.
[Journal]
39)  Kireeva ML, Hancock B, Cremona GH, Walter W, Studitsky VM, Kashlev M.
Nature of the Nucleosomal Barrier to RNA Polymerase II.
Molecular Cell. 18: 97-108, 2005.
[Journal]
40)  Studitsky VM, Walter W, Kireeva M, Kashlev M, Felsenfeld G.
Chromatin Remodeling by RNA Polymerase (review).
Trends Biochem Sci. 29(3): 127-35, 2004.
[Journal]
41)  Walter W, Kashlev M, Studitsky VM.
Transcription through the nucleosome by mRNA-producing RNA polymerases.
Meth. Enzymol. 377: 445-60, 2004.
[Journal]
42)  Walter W, Kireeva ML, Tchernajenko V, Kashlev M, Studitsky VM.
). The fate of the Nucleosome during Transcription by RNA Polymerase II.
Methods in Enzymology. 371: 564-577, 2003.
[Journal]
43)  Walter W, Kireeva ML, Studitsky VM, Kashlev M.
Bacterial and yeast RNA Polymerase II Use Similar Mechanism for Transcription through Nucleosomes.
J. Biol. Chem. 278: 36148-36156, 2003.
[Journal]
44)  Mustaev A, Zaychikov E, Grachev M, Kozlov M, Severinov K, Epshtein V, Korzheva N, Bereshchenko O, Markovtsov V, Lukhtanov E, Tsarev I, Maximova T, Kashlev M, Bass I, Nikiforov V, Goldfarb A.
Cross-linking Studies of RNA Polymerase Active Center. Methods and Strategies.
Methods in Enzymology. 371: 191-206, 2003.
[Journal]
45)  Kireeva ML, Lubkowska L, Komissarova N, Kashlev M.
Double-tagged RNA Polymerase II from Saccharomyces cerevisiae: Assays and Affinity Purification of Biotinylated and Non-Biotinylated Forms of Core Enzyme.
Methods in Enzymology. 370: 138-155, 2003.
[Journal]
46)  Komissarova N, Kireeva ML, Becker J, Sidorenkov I, Kashlev M.
Engineering of Elongation Complexes of Bacterial and Yeast RNA Polymerases .
Methods in Enzymology. 371: 233-251, 2003.
[Journal]
47)  Karamychev VN, Tatusov A, Komissarova N, Kashlev M, Neumann RD, Zhurkin VB, Panyutin IG.
Iodine-125 Radioprobing of E. coli RNA Polymerase Transcription Elongation Complexes.
Methods in Enzymology. 371: 106-120, 2003.
[Journal]
48)  Kireeva ML, Walter W, Tchernajenko V, Bondarenko V, Kashlev M, Studitsky VM.
Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription.
Molecular Cell. 9: 541-552, 2002.
[Journal]
49)  Komissarova N, Becker J, Solter S, Kireeva M, Kashlev M.
Shortening of RNA:DNA Hybrid in Elongation Complex of RNA Polymerase Is a Prerequisite for Transcription Termination.
Molecular Cell. 10(5): 1151-1162, 2002.
[Journal]
50)  Kashlev M, Komissarova N.
Transcription termination: primary intermediates and secondary adducts.
J Biol Chem. 277: 14501-14508, 2002.
[Journal]
51)  Kireeva ML, Komissarova N, Kashlev M.
Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity.
J Mol Biol. 299: 325-335, 2000.
[Journal]
52)  Kireeva ML, Komissarova N, Waugh DS, Kashlev M.
The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex.
J Biol Chem. 275: 6530-6536, 2000.
[Journal]
53)  Thomson NH, Smith BL, Almqvist N, Schmitt L, Kashlev M, Kool ET, Hansma PK.
Oriented, active Escherichia coli RNA polymerase: an atomic force microscope study.
Biophys. J. 76: 1024-33, 1999.
[Journal]
54)  Sidorenkov I, Komissarova N, Kashlev M.
Crucial role of the RNA:DNA hybrid in the processivity of transcription.
Molecular Cell. 2: 55-64, 1998.
[Journal]
55)  Komissarova N, Kashlev M.
Functional topography of nascent RNA in elongation intermediates of RNA polymerase.
Proc Natl Acad Sci USA. 95(25): 14699-704, 1998.
[Journal]
56)  Kasas S, Thomson NH, Smith BL, Hansma HG, Zhu X, Guthold M, Bustamante C, Kool ET, Kashlev M, Hansma PK.
Escherichia coli RNA polymerase activity observed using atomic force microscopy.
Biochemistry. 36: 461-8, 1997.
[Journal]
57)  Alekshun M, Kashlev M, Schwartz I.
Molecular cloning and characterization of Borrelia burgdorferi rpoB.
Gene. 186: 227-35, 1997.
[Journal]
58)  Komissarova N, Kashlev M.
RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA.
J. Biol. Chem. 272: 15329-38, 1997.
[Journal]
59)  Komissarova N, Kashlev M.
Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded.
Proc. Natl. Acad. Sci. U.S.A. 94: 1755-60, 1997.
[Journal]
60)  Kashlev M, Nudler E, Severinov K, Borukhov S, Komissarova N, Goldfarb A.
Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase.
Meth. Enzymol. 274: 326-34, 1996.
[Journal]
61)  Zaychikov E, Martin E, Denissova L, Kozlov M, Markovtsov V, Kashlev M, Heumann H, Nikiforov V, Goldfarb A, Mustaev A.
Mapping of catalytic residues in the RNA polymerase active center.
Science. 273: 107-9, 1996.
[Journal]
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This page was last updated on 5/27/2014.