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. ncbi request reprint Transcription. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications12

  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. ncbi request reprint Transcription. 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...
  7. 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...
  8. 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...
  9. 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...
  10. 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
    ....
  11. 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...
  12. ncbi request reprint 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. ..