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Detection of spacer precursors formed in vivo during primed CRISPR adaptation.

Shiriaeva AA, Savitskaya E, Datsenko KA, Vvedenskaya IO, Fedorova I, Morozova N, Metlitskaya A, Sabantsev A, Nickels BE, Severinov K, Semenova E.

Nat Commun. 2019 Oct 10;10(1):4603. doi: 10.1038/s41467-019-12417-w.


Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase.

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.

Elife. 2018 Dec 12;7. pii: e42179. doi: 10.7554/eLife.42179.


Analysis of Bacterial Transcription by "Massively Systematic Transcript End Readout," MASTER.

Vvedenskaya IO, Goldman SR, Nickels BE.

Methods Enzymol. 2018;612:269-302. doi: 10.1016/bs.mie.2018.09.007. Epub 2018 Oct 12.


Role for GrgA in Regulation of σ28-Dependent Transcription in the Obligate Intracellular Bacterial Pathogen Chlamydia trachomatis.

Desai M, Wurihan W, Di R, Fondell JD, Nickels BE, Bao X, Fan H.

J Bacteriol. 2018 Sep 24;200(20). pii: e00298-18. doi: 10.1128/JB.00298-18. Print 2018 Oct 15.


"NAD-capQ" detection and quantitation of NAD caps.

Grudzien-Nogalska E, Bird JG, Nickels BE, Kiledjian M.

RNA. 2018 Oct;24(10):1418-1425. doi: 10.1261/rna.067686.118. Epub 2018 Jul 25.


CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5' Capping with NAD<sup/>.

Vvedenskaya IO, Bird JG, Zhang Y, Zhang Y, Jiao X, Barvík I, Krásný L, Kiledjian M, Taylor DM, Ebright RH, Nickels BE.

Mol Cell. 2018 May 3;70(3):553-564.e9. doi: 10.1016/j.molcel.2018.03.014. Epub 2018 Apr 19.


The mechanism of variability in transcription start site selection.

Yu L, Winkelman JT, Pukhrambam C, Strick TR, Nickels BE, Ebright RH.

Elife. 2017 Nov 23;6. pii: e32038. doi: 10.7554/eLife.32038.


5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding.

Jiao X, Doamekpor SK, Bird JG, Nickels BE, Tong L, Hart RP, Kiledjian M.

Cell. 2017 Mar 9;168(6):1015-1027.e10. doi: 10.1016/j.cell.2017.02.019.


Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence.

Garner AL, Rammohan J, Huynh JP, Onder LM, Chen J, Bae B, Jensen D, Weiss LA, Manzano AR, Darst SA, Campbell EA, Nickels BE, Galburt EA, Stallings CL.

J Bacteriol. 2017 Jan 30;199(4). pii: e00698-16. doi: 10.1128/JB.00698-16. Print 2017 Feb 15.


The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA.

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.

Nature. 2016 Jul 21;535(7612):444-7. Epub 2016 Jul 6.


Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection.

Vvedenskaya IO, Vahedian-Movahed H, Zhang Y, Taylor DM, Ebright RH, Nickels BE.

Proc Natl Acad Sci U S A. 2016 May 24;113(21):E2899-905. doi: 10.1073/pnas.1603271113. Epub 2016 May 9.


Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.

Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE.

Science. 2016 Mar 4;351(6277):1090-3. doi: 10.1126/science.aad6881.


tRNA is a new target for cleavage by a MazF toxin.

Schifano JM, Cruz JW, Vvedenskaya IO, Edifor R, Ouyang M, Husson RN, Nickels BE, Woychik NA.

Nucleic Acids Res. 2016 Feb 18;44(3):1256-70. doi: 10.1093/nar/gkv1370. Epub 2016 Jan 5.


Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields.

Vvedenskaya IO, Zhang Y, Goldman SR, Valenti A, Visone V, Taylor DM, Ebright RH, Nickels BE.

Mol Cell. 2015 Dec 17;60(6):953-65. doi: 10.1016/j.molcel.2015.10.029. Epub 2015 Nov 25.


The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo.

Goldman SR, Nair NU, Wells CD, Nickels BE, Hochschild A.

Elife. 2015 Sep 15;4. doi: 10.7554/eLife.10514.


Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase.

Cruz JW, Sharp JD, Hoffer ED, Maehigashi T, Vvedenskaya IO, Konkimalla A, Husson RN, Nickels BE, Dunham CM, Woychik NA.

Nat Commun. 2015 Jul 9;6:7480. doi: 10.1038/ncomms8480.


A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.

Druzhinin SY, Tran NT, Skalenko KS, Goldman SR, Knoblauch JG, Dove SL, Nickels BE.

PLoS Genet. 2015 Jul 1;11(7):e1005348. doi: 10.1371/journal.pgen.1005348. eCollection 2015 Jul.


Ubiquitous promoter-localization of essential virulence regulators in Francisella tularensis.

Ramsey KM, Osborne ML, Vvedenskaya IO, Su C, Nickels BE, Dove SL.

PLoS Pathog. 2015 Apr 1;11(4):e1004793. doi: 10.1371/journal.ppat.1004793. eCollection 2015 Apr.


Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends.

Vvedenskaya IO, Goldman SR, Nickels BE.

Methods Mol Biol. 2015;1276:211-28. doi: 10.1007/978-1-4939-2392-2_12.


Interactions between RNA polymerase and the "core recognition element" counteract pausing.

Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR, Zhang Y, Ebright RH, Nickels BE.

Science. 2014 Jun 13;344(6189):1285-9. doi: 10.1126/science.1253458.


An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3.

Schifano JM, Vvedenskaya IO, Knoblauch JG, Ouyang M, Nickels BE, Woychik NA.

Nat Commun. 2014 Apr 8;5:3538. doi: 10.1038/ncomms4538.


Structure of the DNA-binding and RNA-polymerase-binding region of transcription antitermination factor λQ.

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. 2014 Mar 4;22(3):488-95. doi: 10.1016/j.str.2013.12.010. Epub 2014 Jan 16.


A new way to start: nanoRNA-mediated priming of transcription initiation.

Nickels BE.

Transcription. 2012 Nov-Dec;3(6):300-4. doi: 10.4161/trns.21903. Epub 2012 Nov 1.


Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of σ66.

Bao X, Nickels BE, Fan H.

Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):16870-5. doi: 10.1073/pnas.1207300109. Epub 2012 Oct 1.


Interaction of CarD with RNA polymerase mediates Mycobacterium tuberculosis viability, rifampin resistance, and pathogenesis.

Weiss LA, Harrison PG, Nickels BE, Glickman MS, Campbell EA, Darst SA, Stallings CL.

J Bacteriol. 2012 Oct;194(20):5621-31. Epub 2012 Aug 17.


Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs.

Vvedenskaya IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, Nickels BE.

Genes Dev. 2012 Jul 1;26(13):1498-507. doi: 10.1101/gad.192732.112.


A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing.

Berdygulova Z, Esyunina D, Miropolskaya N, Mukhamedyarov D, Kuznedelov K, Nickels BE, Severinov K, Kulbachinskiy A, Minakhin L.

Nucleic Acids Res. 2012 May;40(9):4052-63. doi: 10.1093/nar/gkr1285. Epub 2012 Jan 11.


Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis.

Bao X, Pachikara ND, Oey CB, Balakrishnan A, Westblade LF, Tan M, Chase T Jr, Nickels BE, Fan H.

Microbiology. 2011 Sep;157(Pt 9):2569-81. doi: 10.1099/mic.0.049668-0. Epub 2011 Jun 30.


NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria.

Nickels BE, Dove SL.

J Mol Biol. 2011 Oct 7;412(5):772-81. doi: 10.1016/j.jmb.2011.06.015. Epub 2011 Jun 16.


NanoRNAs prime transcription initiation in vivo.

Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE.

Mol Cell. 2011 Jun 24;42(6):817-25. doi: 10.1016/j.molcel.2011.06.005.


A novel method for the production of in vivo-assembled, recombinant Escherichia coli RNA polymerase lacking the α C-terminal domain.

Twist KA, Husnain SI, Franke JD, Jain D, Campbell EA, Nickels BE, Thomas MS, Darst SA, Westblade LF.

Protein Sci. 2011 Jun;20(6):986-95. doi: 10.1002/pro.622. Epub 2011 Apr 26.


Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex.

Deighan P, Pukhrambam C, Nickels BE, Hochschild A.

Genes Dev. 2011 Jan 1;25(1):77-88. doi: 10.1101/gad.1991811.


Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.

Westblade LF, Campbell EA, Pukhrambam C, Padovan JC, Nickels BE, Lamour V, Darst SA.

Nucleic Acids Res. 2010 Dec;38(22):8357-69. doi: 10.1093/nar/gkq692. Epub 2010 Aug 11.


Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation.

Devi PG, Campbell EA, Darst SA, Nickels BE.

Mol Microbiol. 2010 Feb;75(3):607-22. doi: 10.1111/j.1365-2958.2009.07021.x. Epub 2010 Jan 12.


A new twist on a classic paradigm: illumination of a genetic switch in Vibrio cholerae phage CTX Phi.

Nickels BE.

J Bacteriol. 2009 Nov;191(22):6779-81. doi: 10.1128/JB.01150-09. Epub 2009 Sep 11. No abstract available.


CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence.

Stallings CL, Stephanou NC, Chu L, Hochschild A, Nickels BE, Glickman MS.

Cell. 2009 Jul 10;138(1):146-59. doi: 10.1016/j.cell.2009.04.041.


Direct detection of abortive RNA transcripts in vivo.

Goldman SR, Ebright RH, Nickels BE.

Science. 2009 May 15;324(5929):927-8. doi: 10.1126/science.1169237.


The bacteriophage T4 AsiA protein contacts the beta-flap domain of RNA polymerase.

Yuan AH, Nickels BE, Hochschild A.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6597-602. doi: 10.1073/pnas.0812832106. Epub 2009 Apr 6.


Genetic assays to define and characterize protein-protein interactions involved in gene regulation.

Nickels BE.

Methods. 2009 Jan;47(1):53-62. doi: 10.1016/j.ymeth.2008.10.011. Epub 2008 Oct 24. Review.


The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase.

Deighan P, Diez CM, Leibman M, Hochschild A, Nickels BE.

Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15305-10. doi: 10.1073/pnas.0805757105. Epub 2008 Oct 1.


Structural basis for bacterial transcription-coupled DNA repair.

Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, Savery NJ, Darst SA.

Cell. 2006 Feb 10;124(3):507-20.


An altered-specificity DNA-binding mutant of Escherichia coli sigma70 facilitates the analysis of sigma70 function in vivo.

Gregory BD, Nickels BE, Darst SA, Hochschild A.

Mol Microbiol. 2005 Jun;56(5):1208-19.


The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation.

Nickels BE, Garrity SJ, Mekler V, Minakhin L, Severinov K, Ebright RH, Hochschild A.

Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4488-93. Epub 2005 Mar 10.


Regulation of RNA polymerase through the secondary channel.

Nickels BE, Hochschild A.

Cell. 2004 Aug 6;118(3):281-4. Review.


The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter.

Nickels BE, Mukhopadhyay J, Garrity SJ, Ebright RH, Hochschild A.

Nat Struct Mol Biol. 2004 Jun;11(6):544-50. Epub 2004 May 2.


A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme.

Gregory BD, Nickels BE, Garrity SJ, Severinova E, Minakhin L, Urbauer RJ, Urbauer JL, Heyduk T, Severinov K, Hochschild A.

Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4554-9. Epub 2004 Mar 22.


Structure of a ternary transcription activation complex.

Jain D, Nickels BE, Sun L, Hochschild A, Darst SA.

Mol Cell. 2004 Jan 16;13(1):45-53.


Protein-protein and protein-DNA interactions of sigma70 region 4 involved in transcription activation by lambdacI.

Nickels BE, Dove SL, Murakami KS, Darst SA, Hochschild A.

J Mol Biol. 2002 Nov 15;324(1):17-34.


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