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Bryce E. Nickels, PhD

Publications since 2011

Vvedenskaya, I. O. Vahedian-Movahed, H. Zhang, Y. Taylor, D. M. Ebright, R. H. Nickels, B. E. Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. Proc Natl Acad Sci U S A, In process, . (PMID: 27162333)

Winkelman, J. T. Vvedenskaya, I. O. Zhang, Y. Zhang, Y. Bird, J. G. Taylor, D. M. Gourse, R. L. Ebright, R. H. Nickels, B. E. Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science, 351:1090-1093, . (PMID: 26941320)

Schifano, J. M. Cruz, J. W. Vvedenskaya, I. O. Edifor, R. Ouyang, M. Husson, R. N. Nickels, B. E. Woychik, N. A. tRNA is a new target for cleavage by a MazF toxin. Nucleic Acids Res, In process, . (PMID: 26740583)

Vvedenskaya, I. O. Zhang, Y. Goldman, S. R. Valenti, A. Visone, V. Taylor, D. M. Ebright, R. H. Nickels, B. E. Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields. Mol Cell, In process, . (PMID: 26626484)

Goldman, S. R. Nair, N. U. Wells, C. D. Nickels, B. E. Hochschild, A. The primary sigma factor in can access the transcription elongation complex from solution . Elife, In process, . (PMID: 26371553)

Druzhinin, S. Y. Tran, N. T. Skalenko, K. S. Goldman, S. R. Knoblauch, J. G. Dove, S. L. Nickels, B. E. A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq. PLoS Genet, 11:e1005348, . (PMID: 26131907)

Ramsey, K. M. Osborne, M. L. Vvedenskaya, I. O. Su, C. Nickels, B. E. Dove, S. L. Ubiquitous Promoter-Localization of Essential Virulence Regulators in Francisella tularensis. PLoS Pathog, 11:e1004793, . (PMID: 25830507)

Vvedenskaya, I. O. Goldman, S. R. Nickels, B. E. Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends. Methods Mol Biol, 1276:211-228, . (PMID: 25665566)

Cruz, J. W. Sharp, J. D. Hoffer, E. D. Maehigashi, T. Vvedenskaya, I. O. Konkimalla, A. Husson, R. N. Nickels, B. E. Dunham, C. M. Woychik, N. A. Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nat Commun, 6:7480, . (PMID: 26158745)

Vvedenskaya, I. O. Vahedian-Movahed, H. Bird, J. G. Knoblauch, J. G. Goldman, S. R. Zhang, Y. Ebright, R. H. Nickels, B. E. Transcription. Interactions between RNA polymerase and the "core recognition element" counteract pausing. Science, 344:1285-1289, . (PMID: 24926020)

Vorobiev, S. M. Gensler, Y. Vahedian-Movahed, H. Seetharaman, J. Su, M. Huang, J. Y. Xiao, R. Kornhaber, G. Montelione, G. T. Tong, L. Ebright, R. H. Nickels, B. E. Structure of the DNA-Binding and RNA-Polymerase-Binding Region of Transcription Antitermination Factor lambdaQ. Structure, 22:488-495, . (PMID: 24440517, PMCID: PMC3951671)

Schifano, J. M. Vvedenskaya, I. O. Knoblauch, J. G. Ouyang, M. Nickels, B. E. Woychik, N. A. An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. Nat Commun, 5:3538, . (PMID: 24709835, PMCID: PMC4090939)

Nickels, B. E. A new way to start: nanoRNA-mediated priming of transcription initiation. Transcription, 3:300-304, . (PMID: 23117822, PMCID: PMC3630185)

Bao, X. Nickels, B. E. Fan, H. Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of sigma66. Proc Natl Acad Sci U S A, 109:16870-16875, . (PMID: 23027952, PMCID: PMC3479454)

Weiss, L. A. Harrison, P. G. Nickels, B. E. Glickman, M. S. Campbell, E. A. Darst, S. A. Stallings, C. L. Interaction of CarD with RNA Polymerase Mediates Mycobacterium tuberculosis Viability, Rifampin Resistance, and Pathogenesis. J Bacteriol, 194:5621-5631, . (PMID: 22904282, PMCID: PMC3458692)

Vvedenskaya, I. O. Sharp, J. S. Goldman, S. R. Kanabar, P. N. Livny, J. Dove, S. L. Nickels, B. E. Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. Genes Dev, 26:1498-1507, . (PMID: 22751503, PMCID: PMC3403017)

Berdygulova, Z. Esyunina, D. Miropolskaya, N. Mukhamedyarov, D. Kuznedelov, K. Nickels, B. E. Severinov, K. Kulbachinskiy, A. Minakhin, L. A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing. Nucleic Acids Res, 40:4052-4063, . (PMID: 22238378, PMCID: PMC3351154)

Nickels, B. E. Dove, S. L. NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria. J Mol Biol, 412:772-781, . (PMID: 21704045, PMCID: PMC3184357)

Bao, X. Pachikara, N. D. Oey, C. B. Balakrishnan, A. Westblade, L. F. Tan, M. Chase, T. Jr Nickels, B. E. Fan, H. Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis. Microbiology, 157:2569-2581, . (PMID: 21719536, PMCID: PMC3352175)

Goldman, S. R. Sharp, J. S. Vvedenskaya, I. O. Livny, J. Dove, S. L. Nickels, B. E. NanoRNAs prime transcription initiation in vivo. Mol Cell, 42:817-825, . (PMID: 21700226, PMCID: PMC3130991)

Twist, K. A. Husnain, S. I. Franke, J. D. Jain, D. Campbell, E. A. Nickels, B. E. Thomas, M. S. Darst, S. A. Westblade, L. F. A novel method for the production of in vivo-assembled, recombinant Escherichia coli RNA polymerase lacking the alpha C-terminal domain. Protein Sci, 20:986-995, . (PMID: 21416542, PMCID: PMC3104228)

Deighan, P. Pukhrambam, C. Nickels, B. E. Hochschild, A. Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex. Genes Dev, 25:77-88, . (PMID: 21205867, PMCID: PMC3012938)