Bryce E Nickels

Summary

Affiliation: Rutgers University
Country: USA

Publications

  1. doi request reprint Genetic assays to define and characterize protein-protein interactions involved in gene regulation
    Bryce E Nickels
    Waksman Institute and Department of Genetics, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, United States
    Methods 47:53-62. 2009
  2. pmc NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria
    Bryce E Nickels
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    J Mol Biol 412:772-81. 2011
  3. pmc A new way to start: nanoRNA-mediated priming of transcription initiation
    Bryce E Nickels
    Waksman Institute and Department of Genetics, Rutgers University, Piscataway, NJ, USA
    Transcription 3:300-4. 2012
  4. pmc A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing
    Zhanna Berdygulova
    Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
    Nucleic Acids Res 40:4052-63. 2012
  5. pmc Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs
    Irina O Vvedenskaya
    Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA
    Genes Dev 26:1498-507. 2012
  6. pmc tRNA is a new target for cleavage by a MazF toxin
    Jason M Schifano
    Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, USA
    Nucleic Acids Res 44:1256-70. 2016
  7. pmc Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection
    Jared T Winkelman
    Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA Department of Bacteriology, University of Wisconsin Madison, Madison, WI 53705, USA
    Science 351:1090-3. 2016
  8. pmc Interactions between RNA polymerase and the "core recognition element" counteract pausing
    Irina O Vvedenskaya
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 344:1285-9. 2014
  9. pmc Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation
    Pukhrambam Grihanjali Devi
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Mol Microbiol 75:607-22. 2010
  10. pmc Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection
    Irina O Vvedenskaya
    Department of Genetics, Rutgers University, Piscataway, NJ 08854 Waksman Institute, Rutgers University, Piscataway, NJ 08854
    Proc Natl Acad Sci U S A 113:E2899-905. 2016

Collaborators

Detail Information

Publications19

  1. doi request reprint Genetic assays to define and characterize protein-protein interactions involved in gene regulation
    Bryce E Nickels
    Waksman Institute and Department of Genetics, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, United States
    Methods 47:53-62. 2009
    ..Furthermore, these assays often enable the study of substitutions in essential domains of RNAP that would be lethal in their natural context...
  2. pmc NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria
    Bryce E Nickels
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    J Mol Biol 412:772-81. 2011
    ..In this perspective, we summarize the findings of Goldman et al. and discuss the prospect that nanoRNA-mediated priming of transcription initiation represents an underappreciated aspect of gene expression in vivo...
  3. pmc A new way to start: nanoRNA-mediated priming of transcription initiation
    Bryce E Nickels
    Waksman Institute and Department of Genetics, Rutgers University, Piscataway, NJ, USA
    Transcription 3:300-4. 2012
    ..Priming of transcription initiation with nanoRNAs represents a previously undocumented component of transcription start site selection and gene expression...
  4. pmc A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing
    Zhanna Berdygulova
    Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
    Nucleic Acids Res 40:4052-63. 2012
    ..To our knowledge, gp39 is the first characterized phage-encoded transcription factor that affects every step of the transcription cycle and suppresses transcription termination through its antipausing activity...
  5. pmc Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs
    Irina O Vvedenskaya
    Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA
    Genes Dev 26:1498-507. 2012
    ..In addition, our findings identify nanoRNAs as a previously undocumented class of regulatory small RNAs that function by being directly incorporated into a target transcript...
  6. pmc tRNA is a new target for cleavage by a MazF toxin
    Jason M Schifano
    Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, USA
    Nucleic Acids Res 44:1256-70. 2016
    ..Our data also suggest a role for tRNA distinct from its canonical adapter function in translation, as cleavage of tRNAs by MazF-mt9 downregulates bacterial growth. ..
  7. pmc Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection
    Jared T Winkelman
    Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA Department of Bacteriology, University of Wisconsin Madison, Madison, WI 53705, USA
    Science 351:1090-3. 2016
    ..We propose that TSS selection involves DNA scrunching prior to RNA synthesis. ..
  8. pmc Interactions between RNA polymerase and the "core recognition element" counteract pausing
    Irina O Vvedenskaya
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 344:1285-9. 2014
    ..Our findings identify key sequence determinants of transcriptional pausing and establish that RNAP-CRE interactions modulate pausing...
  9. pmc Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation
    Pukhrambam Grihanjali Devi
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Mol Microbiol 75:607-22. 2010
    ..Thus, our findings suggest that displacement of sigma(4) from core enables the RNA polymerase holoenzyme to adopt a broad range of 'elongation-specific' configurations...
  10. pmc Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection
    Irina O Vvedenskaya
    Department of Genetics, Rutgers University, Piscataway, NJ 08854 Waksman Institute, Rutgers University, Piscataway, NJ 08854
    Proc Natl Acad Sci U S A 113:E2899-905. 2016
    ....
  11. pmc Direct detection of abortive RNA transcripts in vivo
    Seth R Goldman
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 324:927-8. 2009
    ..Abortive transcripts may have functional roles in regulating gene expression in vivo...
  12. ncbi request reprint A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition
    Konstantin Kuznedelov
    Waksman Institute, Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
    Science 295:855-7. 2002
    ..Because the flexible flap is evolutionarily conserved, this domain may facilitate promoter recognition by specificity factors in eukaryotes as well...
  13. pmc A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq
    Sergey Y Druzhinin
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
    PLoS Genet 11:e1005348. 2015
    ..We propose that PDI in both E. coli and V. cholerae occurs though a growth phase-dependent process that leads to the preferential generation of the linear dinucleotides 5´-UA-3´ and 5´-GG-3´. ..
  14. pmc Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields
    Irina O Vvedenskaya
    Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Mol Cell 60:953-65. 2015
    ..The results further reveal that TSSomes depend on DNA topology, consistent with the proposal that TSS selection involves transcription-bubble expansion ("scrunching") and transcription-bubble contraction ("anti-scrunching")...
  15. pmc NanoRNAs prime transcription initiation in vivo
    Seth R Goldman
    Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Mol Cell 42:817-25. 2011
    ....
  16. pmc Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of σ66
    Xiaofeng Bao
    Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
    Proc Natl Acad Sci U S A 109:16870-5. 2012
    ..trachomatis. Furthermore, because GrgA is present only in chlamydiae, our findings highlight how nonconserved regions of the bacterial RNA polymerase can be targets of regulatory factors that are unique to particular organisms...
  17. pmc Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase
    Jonathan W Cruz
    Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Nat Commun 6:7480. 2015
    ..This stress-linked activity of VapC-mt4 mirrors basic features of eukaryotic tRNases that also generate tRNA halves and inhibit translation in response to stress. ..
  18. pmc Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends
    Irina O Vvedenskaya
    Department of Genetics and Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
    Methods Mol Biol 1276:211-28. 2015
    ..5' specific RNA-seq can be used to analyze transcription initiation and posttranscriptional processing of RNAs with single base pair resolution on a genome-wide level. ..
  19. pmc An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3
    Jason M Schifano
    Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Nat Commun 5:3538. 2014
    ..coli, removal of the aSD sequence by a MazF toxin modifies ribosomes to selectively translate leaderless mRNAs in M. tuberculosis. ..