Year |
Citation |
Score |
2024 |
Zhu Y, Vvedenskaya IO, Sze SH, Nickels BE, Kaplan CD. Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels. Nature Structural & Molecular Biology. PMID 38177677 DOI: 10.1038/s41594-023-01171-9 |
0.365 |
|
2022 |
Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH. In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel. Proceedings of the National Academy of Sciences of the United States of America. 119: e2205278119. PMID 35951650 DOI: 10.1073/pnas.2205278119 |
0.335 |
|
2022 |
Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE. Structural and mechanistic basis of σ-dependent transcriptional pausing. Proceedings of the National Academy of Sciences of the United States of America. 119: e2201301119. PMID 35653571 DOI: 10.1073/pnas.2201301119 |
0.378 |
|
2022 |
Liu Y, Yu L, Pukhrambam C, Winkelman JT, Firlar E, Kaelber JT, Zhang Y, Nickels BE, Ebright RH. Structural and mechanistic basis of reiterative transcription initiation. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35082149 DOI: 10.1073/pnas.2115746119 |
0.484 |
|
2021 |
Pukhrambam C, Vvedenskaya IO, Nickels BE. XACT-seq: A photocrosslinking-based technique for detection of the RNA polymerase active-center position relative to DNA in . Star Protocols. 2: 100858. PMID 34693360 DOI: 10.1016/j.xpro.2021.100858 |
0.447 |
|
2021 |
Zhao T, Vvedenskaya IO, Lai WK, Basu S, Pugh BF, Nickels BE, Kaplan CD. Ssl2/TFIIH function in transcription start site scanning by RNA Polymerase II in . Elife. 10. PMID 34652274 DOI: 10.7554/eLife.71013 |
0.434 |
|
2021 |
Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope AL, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE. Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in . Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34187896 DOI: 10.1073/pnas.2106388118 |
0.536 |
|
2020 |
Winkelman JT, Pukhrambam C, Vvedenskaya IO, Zhang Y, Taylor DM, Shah P, Ebright RH, Nickels BE. XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing. Molecular Cell. PMID 32750314 DOI: 10.1016/J.Molcel.2020.07.006 |
0.739 |
|
2020 |
Vvedenskaya IO, Nickels BE. CapZyme-Seq: A 5'-RNA-Seq Method for Differential Detection and Quantitation of NAD-Capped and Uncapped 5'-Triphosphate RNA. Star Protocols. 1. PMID 32719830 DOI: 10.1016/j.xpro.2019.100002 |
0.398 |
|
2020 |
Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, ... ... Nickels BE, et al. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biology. 21: 132. PMID 32487207 DOI: 10.1186/S13059-020-02040-0 |
0.507 |
|
2020 |
Yadavalli SS, Goh T, Carey JN, Malengo G, Vellappan S, Nickels BE, Sourjik V, Goulian M, Yuan J. Functional determinants of a small protein controlling a broadly conserved bacterial sensor kinase. Journal of Bacteriology. PMID 32482726 DOI: 10.1128/Jb.00305-20 |
0.378 |
|
2019 |
Shiriaeva AA, Savitskaya E, Datsenko KA, Vvedenskaya IO, Fedorova I, Morozova N, Metlitskaya A, Sabantsev A, Nickels BE, Severinov K, Semenova E. Detection of spacer precursors formed in vivo during primed CRISPR adaptation. Nature Communications. 10: 4603. PMID 31601800 DOI: 10.1038/S41467-019-12417-W |
0.317 |
|
2018 |
Bird JG, Basu U, Kuster D, Ramachandran A, Grudzien-Nogalska E, Towheed A, Wallace DC, Kiledjian M, Temiakov D, Patel SS, Ebright RH, Nickels BE. Highly efficient 5' capping of mitochondrial RNA with NAD and NADH by yeast and human mitochondrial RNA polymerase. Elife. 7. PMID 30526856 DOI: 10.7554/Elife.42179 |
0.505 |
|
2018 |
Vvedenskaya IO, Goldman SR, Nickels BE. Analysis of Bacterial Transcription by "Massively Systematic Transcript End Readout," MASTER. Methods in Enzymology. 612: 269-302. PMID 30502946 DOI: 10.1016/Bs.Mie.2018.09.007 |
0.556 |
|
2018 |
Desai M, Wurihan W, Di R, Fondell JD, Nickels BE, Bao X, Fan H. A role for GrgA in regulation of σ-dependent transcription in the obligate intracellular bacterial pathogen . Journal of Bacteriology. PMID 30061357 DOI: 10.1128/Jb.00298-18 |
0.57 |
|
2018 |
Grudzien-Nogalska E, Bird JG, Nickels B, Kiledjian M. 'NAD-capQ' Detection and Quantitation of NAD caps. Rna (New York, N.Y.). PMID 30045887 DOI: 10.1261/Rna.067686.118 |
0.448 |
|
2018 |
Vvedenskaya IO, Bird JG, Zhang Y, Zhang Y, Jiao X, Barvík I, Krásný L, Kiledjian M, Taylor DM, Ebright RH, Nickels BE. CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5' Capping with NAD. Molecular Cell. PMID 29681497 DOI: 10.1016/J.Molcel.2018.03.014 |
0.73 |
|
2018 |
Bird JG, Basu U, Kuster D, Ramachandran A, Grudzien-Nogalska E, Towheed A, Wallace DC, Kiledjian M, Temiakov D, Patel SS, Ebright RH, Nickels BE. Author response: Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase Elife. DOI: 10.7554/Elife.42179.023 |
0.403 |
|
2017 |
Yu L, Winkelman J, Pukhrambam C, Strick T, Nickels BE, Ebright RH. The mechanism of variability in transcription start site selection. Elife. 6. PMID 29168694 DOI: 10.7554/Elife.32038 |
0.531 |
|
2017 |
Bird JG, Nickels BE, Ebright RH. RNA Capping by Transcription Initiation with Non-canonical Initiating Nucleotides (NCINs): Determination of Relative Efficiencies of Transcription Initiation with NCINs and NTPs. Bio-Protocol. 7. PMID 28840175 DOI: 10.21769/BioProtoc.2336 |
0.511 |
|
2017 |
Jiao X, Doamekpor SK, Bird JG, Nickels BE, Tong L, Hart RP, Kiledjian M. 5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding. Cell. 168: 1015-1027.e10. PMID 28283058 DOI: 10.1016/J.Cell.2017.02.019 |
0.494 |
|
2017 |
Yu L, Winkelman JT, Pukhrambam C, Strick TR, Nickels BE, Ebright RH. Author response: The mechanism of variability in transcription start site selection Elife. DOI: 10.7554/Elife.32038.019 |
0.361 |
|
2016 |
Garner AL, Rammohan J, Huynh JP, Onder LM, Chen J, Bae B, Jensen D, Weiss LA, Ruiz Manzano A, Darst SA, Campbell EA, Nickels BE, Galburt EA, Stallings CL. Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence. Journal of Bacteriology. PMID 27920294 DOI: 10.1128/Jb.00698-16 |
0.494 |
|
2016 |
Bird JG, Zhang Y, Tian Y, Panova N, Barvík I, Greene L, Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, Nickels BE. The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA. Nature. PMID 27383794 DOI: 10.1038/Nature18622 |
0.592 |
|
2016 |
Vvedenskaya IO, Vahedian-Movahed H, Zhang Y, Taylor DM, Ebright RH, Nickels BE. Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. Proceedings of the National Academy of Sciences of the United States of America. PMID 27162333 DOI: 10.1073/Pnas.1603271113 |
0.763 |
|
2016 |
Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE. Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science (New York, N.Y.). 351: 1090-3. PMID 26941320 DOI: 10.1126/Science.Aad6881 |
0.729 |
|
2016 |
Schifano JM, Cruz JW, Vvedenskaya IO, Edifor R, Ouyang M, Husson RN, Nickels BE, Woychik NA. tRNA is a new target for cleavage by a MazF toxin. Nucleic Acids Research. 44: 1256-70. PMID 26740583 DOI: 10.1093/Nar/Gkv1370 |
0.457 |
|
2015 |
Vvedenskaya IO, Zhang Y, Goldman SR, Valenti A, Visone V, Taylor DM, Ebright RH, Nickels BE. Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields. Molecular Cell. PMID 26626484 DOI: 10.1016/J.Molcel.2015.10.029 |
0.739 |
|
2015 |
Goldman SR, Nair NU, Wells CD, Nickels BE, Hochschild A. The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo. Elife. 4. PMID 26371553 DOI: 10.7554/Elife.10514 |
0.728 |
|
2015 |
Cruz JW, Sharp JD, Hoffer ED, Maehigashi T, Vvedenskaya IO, Konkimalla A, Husson RN, Nickels BE, Dunham CM, Woychik NA. Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nature Communications. 6: 7480. PMID 26158745 DOI: 10.1038/Ncomms8480 |
0.341 |
|
2015 |
Druzhinin SY, Tran NT, Skalenko KS, Goldman SR, Knoblauch JG, Dove SL, Nickels BE. A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq. Plos Genetics. 11: e1005348. PMID 26131907 DOI: 10.1371/Journal.Pgen.1005348 |
0.731 |
|
2015 |
Ramsey KM, Osborne ML, Vvedenskaya IO, Su C, Nickels BE, Dove SL. Ubiquitous promoter-localization of essential virulence regulators in Francisella tularensis. Plos Pathogens. 11: e1004793. PMID 25830507 DOI: 10.1371/Journal.Ppat.1004793 |
0.766 |
|
2015 |
Vvedenskaya IO, Goldman SR, Nickels BE. Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends. Methods in Molecular Biology (Clifton, N.J.). 1276: 211-28. PMID 25665566 DOI: 10.1007/978-1-4939-2392-2_12 |
0.502 |
|
2015 |
Goldman SR, Nair NU, Wells CD, Nickels BE, Hochschild A. Author response: The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo Elife. DOI: 10.7554/Elife.10514.011 |
0.644 |
|
2015 |
Ramsey KM, Osborne ML, Vvedenskaya IO, Su C, Nickels BE, Dove SL. Ubiquitous Promoter-Localization of Essential Virulence Regulators in Francisella tularensis Plos Pathogens. 11. DOI: 10.1371/journal.ppat.1004793 |
0.646 |
|
2014 |
Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR, Zhang Y, Ebright RH, Nickels BE. Transcription. Interactions between RNA polymerase and the "core recognition element" counteract pausing. Science (New York, N.Y.). 344: 1285-9. PMID 24926020 DOI: 10.1126/Science.1253458 |
0.624 |
|
2014 |
Schifano JM, Vvedenskaya IO, Knoblauch JG, Ouyang M, Nickels BE, Woychik NA. An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. Nature Communications. 5: 3538. PMID 24709835 DOI: 10.1038/Ncomms4538 |
0.5 |
|
2014 |
Vorobiev SM, Gensler Y, Vahedian-Movahed H, Seetharaman J, Su M, Huang JY, Xiao R, Kornhaber G, Montelione GT, Tong L, Ebright RH, Nickels BE. Structure of the DNA-binding and RNA-polymerase-binding region of transcription antitermination factor λQ. Structure (London, England : 1993). 22: 488-95. PMID 24440517 DOI: 10.1016/J.Str.2013.12.010 |
0.607 |
|
2012 |
Nickels BE. A new way to start: nanoRNA-mediated priming of transcription initiation. Transcription. 3: 300-4. PMID 23117822 DOI: 10.4161/trns.21903 |
0.518 |
|
2012 |
Bao X, Nickels BE, Fan H. Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of σ66. Proceedings of the National Academy of Sciences of the United States of America. 109: 16870-5. PMID 23027952 DOI: 10.1073/Pnas.1207300109 |
0.597 |
|
2012 |
Weiss LA, Harrison PG, Nickels BE, Glickman MS, Campbell EA, Darst SA, Stallings CL. Interaction of CarD with RNA polymerase mediates Mycobacterium tuberculosis viability, rifampin resistance, and pathogenesis. Journal of Bacteriology. 194: 5621-31. PMID 22904282 DOI: 10.1128/Jb.00879-12 |
0.414 |
|
2012 |
Vvedenskaya IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, Nickels BE. Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. Genes & Development. 26: 1498-507. PMID 22751503 DOI: 10.1101/Gad.192732.112 |
0.771 |
|
2012 |
Berdygulova Z, Esyunina D, Miropolskaya N, Mukhamedyarov D, Kuznedelov K, Nickels BE, Severinov K, Kulbachinskiy A, Minakhin L. A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing. Nucleic Acids Research. 40: 4052-63. PMID 22238378 DOI: 10.1093/Nar/Gkr1285 |
0.579 |
|
2011 |
Bao X, Pachikara ND, Oey CB, Balakrishnan A, Westblade LF, Tan M, Chase T, Nickels BE, Fan H. Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis. Microbiology (Reading, England). 157: 2569-81. PMID 21719536 DOI: 10.1099/Mic.0.049668-0 |
0.354 |
|
2011 |
Nickels BE, Dove SL. NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria. Journal of Molecular Biology. 412: 772-81. PMID 21704045 DOI: 10.1016/J.Jmb.2011.06.015 |
0.756 |
|
2011 |
Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE. NanoRNAs prime transcription initiation in vivo. Molecular Cell. 42: 817-25. PMID 21700226 DOI: 10.1016/J.Molcel.2011.06.005 |
0.777 |
|
2011 |
Twist KA, Husnain SI, Franke JD, Jain D, Campbell EA, Nickels BE, Thomas MS, Darst SA, Westblade LF. A novel method for the production of in vivo-assembled, recombinant Escherichia coli RNA polymerase lacking the α C-terminal domain. Protein Science : a Publication of the Protein Society. 20: 986-95. PMID 21416542 DOI: 10.1002/Pro.622 |
0.463 |
|
2011 |
Deighan P, Pukhrambam C, Nickels BE, Hochschild A. Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex. Genes & Development. 25: 77-88. PMID 21205867 DOI: 10.1101/Gad.1991811 |
0.748 |
|
2010 |
Westblade LF, Campbell EA, Pukhrambam C, Padovan JC, Nickels BE, Lamour V, Darst SA. Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction. Nucleic Acids Research. 38: 8357-69. PMID 20702425 DOI: 10.1093/Nar/Gkq692 |
0.569 |
|
2010 |
Devi PG, Campbell EA, Darst SA, Nickels BE. Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation. Molecular Microbiology. 75: 607-22. PMID 20070531 DOI: 10.1111/J.1365-2958.2009.07021.X |
0.597 |
|
2009 |
Nickels BE. A new twist on a classic paradigm: illumination of a genetic switch in Vibrio cholerae phage CTX Phi. Journal of Bacteriology. 191: 6779-81. PMID 19749052 DOI: 10.1128/Jb.01150-09 |
0.356 |
|
2009 |
Stallings CL, Stephanou NC, Chu L, Hochschild A, Nickels BE, Glickman MS. CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence. Cell. 138: 146-59. PMID 19596241 DOI: 10.1016/J.Cell.2009.04.041 |
0.708 |
|
2009 |
Goldman SR, Ebright RH, Nickels BE. Direct detection of abortive RNA transcripts in vivo. Science (New York, N.Y.). 324: 927-8. PMID 19443781 DOI: 10.1126/Science.1169237 |
0.624 |
|
2009 |
Yuan AH, Nickels BE, Hochschild A. The bacteriophage T4 AsiA protein contacts the beta-flap domain of RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 106: 6597-602. PMID 19366670 DOI: 10.1073/Pnas.0812832106 |
0.833 |
|
2009 |
Nickels BE. Genetic assays to define and characterize protein-protein interactions involved in gene regulation. Methods (San Diego, Calif.). 47: 53-62. PMID 18952173 DOI: 10.1016/J.Ymeth.2008.10.011 |
0.582 |
|
2008 |
Deighan P, Diez CM, Leibman M, Hochschild A, Nickels BE. The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 105: 15305-10. PMID 18832144 DOI: 10.1073/Pnas.0805757105 |
0.79 |
|
2006 |
Nickels BE, Roberts CW, Roberts JW, Hochschild A. RNA-mediated destabilization of the sigma(70) region 4/beta flap interaction facilitates engagement of RNA polymerase by the Q antiterminator. Molecular Cell. 24: 457-68. PMID 17081994 DOI: 10.1016/J.Molcel.2006.09.014 |
0.771 |
|
2006 |
Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, Savery NJ, Darst SA. Structural basis for bacterial transcription-coupled DNA repair. Cell. 124: 507-20. PMID 16469698 DOI: 10.1016/J.Cell.2005.11.045 |
0.702 |
|
2005 |
Gregory BD, Nickels BE, Darst SA, Hochschild A. An altered-specificity DNA-binding mutant of Escherichia coli sigma70 facilitates the analysis of sigma70 function in vivo. Molecular Microbiology. 56: 1208-19. PMID 15882415 DOI: 10.1111/J.1365-2958.2005.04624.X |
0.777 |
|
2005 |
Nickels BE, Garrity SJ, Mekler V, Minakhin L, Severinov K, Ebright RH, Hochschild A. The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation. Proceedings of the National Academy of Sciences of the United States of America. 102: 4488-93. PMID 15761057 DOI: 10.1073/Pnas.0409850102 |
0.826 |
|
2004 |
Nickels BE, Hochschild A. Regulation of RNA polymerase through the secondary channel. Cell. 118: 281-4. PMID 15294154 DOI: 10.1016/J.Cell.2004.07.021 |
0.687 |
|
2004 |
Nickels BE, Mukhopadhyay J, Garrity SJ, Ebright RH, Hochschild A. The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. Nature Structural & Molecular Biology. 11: 544-50. PMID 15122345 DOI: 10.1038/Nsmb757 |
0.818 |
|
2004 |
Gregory BD, Nickels BE, Garrity SJ, Severinova E, Minakhin L, Urbauer RJ, Urbauer JL, Heyduk T, Severinov K, Hochschild A. A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme. Proceedings of the National Academy of Sciences of the United States of America. 101: 4554-9. PMID 15070756 DOI: 10.1073/Pnas.0400923101 |
0.811 |
|
2004 |
Jain D, Nickels BE, Sun L, Hochschild A, Darst SA. Structure of a ternary transcription activation complex. Molecular Cell. 13: 45-53. PMID 14731393 DOI: 10.1016/S1097-2765(03)00483-0 |
0.714 |
|
2002 |
Nickels BE, Dove SL, Murakami KS, Darst SA, Hochschild A. Protein-protein and protein-DNA interactions of sigma70 region 4 involved in transcription activation by lambdacI. Journal of Molecular Biology. 324: 17-34. PMID 12421556 DOI: 10.1016/S0022-2836(02)01043-4 |
0.797 |
|
2002 |
Nickels BE, Roberts CW, Sun H, Roberts JW, Hochschild A. The sigma(70) subunit of RNA polymerase is contacted by the (lambda)Q antiterminator during early elongation. Molecular Cell. 10: 611-22. PMID 12408828 DOI: 10.1016/S1097-2765(02)00648-2 |
0.708 |
|
2002 |
Pande S, Makela A, Dove SL, Nickels BE, Hochschild A, Hinton DM. The bacteriophage T4 transcription activator MotA interacts with the far-C-terminal region of the sigma70 subunit of Escherichia coli RNA polymerase. Journal of Bacteriology. 184: 3957-64. PMID 12081968 DOI: 10.1128/Jb.184.14.3957-3964.2002 |
0.804 |
|
2002 |
Kuznedelov K, Minakhin L, Niedziela-Majka A, Dove SL, Rogulja D, Nickels BE, Hochschild A, Heyduk T, Severinov K. A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science (New York, N.Y.). 295: 855-7. PMID 11823642 DOI: 10.1126/Science.1066303 |
0.83 |
|
1999 |
Milne JC, Roy RS, Eliot AC, Kelleher NL, Wokhlu A, Nickels B, Walsh CT. Cofactor requirements and reconstitution of microcin B17 synthetase: a multienzyme complex that catalyzes the formation of oxazoles and thiazoles in the antibiotic microcin B17. Biochemistry. 38: 4768-81. PMID 10200165 DOI: 10.1021/Bi982975Q |
0.402 |
|
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