Bryce E. Nickels, Ph.D. - Publications

2002 Harvard University, Cambridge, MA, United States 
Microbiology Biology, Molecular Biology

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.6
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  0.68
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  0.56
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  0.56
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  0.6
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  0.56
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  0.32
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  0.6
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  0.6
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  0.68
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  0.6
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  0.32
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  0.68
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  0.48
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.56
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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