Richard Bonocora

Lecturer, Biological Sciences

Regulation of RNA synthesis is key to the control of gene expression.  In bacteria, RNA is synthesized through the process of transcription by the multi-subunit enzyme RNA polymerase (RNAP).  For proper initiation of transcription, RNAP must temporarily associate with a specificity subunit known as Sigma factor, to recognize a promoter, the site of transcription initiation.  Bacteria can contain several Sigma factors, each differentially activated and responsible for regulating specific sets of genes or regulons.  The development of Next Generation Sequencing techniques such as ChIP-seq and RNA-seq have allowed us to map the binding of multiple Sigma factors across the bacterial genome and determine, at unprecedented resolution, the regulons for each. Unexpectedly, Sigma factor binding and transcription initiation are pervasive; a large fraction of Sigma binding sites occur inside genes. This is contrary to the “textbook” view where promoters are located in between genes and a short distance away from the genes that they control. The role(s) of these “non-canonical” promoters is a mystery, and the next goal is unravel their function on gene expression and the cell lifecycle.


B.S. Biology 1992, State University of New York at Albany; Ph.D. Biology 2004, State University of New York at Albany; Postdoctoral: 2005 - 2010 National Institutes of Health, 2011 - 2015 Wadsworth Center, NYS Department of Health

Research Focus
  • Genomics
  • Molecular Biology
  • Gene Regulation
  • Mobile Genetic Elements
  • STEM Education
Select Works
  • Wong GT, Bonocora RP, Schep AN, Beeler SM, Lee Fong AJ, Shull LM, Batachari LE, Dillon M, Evans C, Becker CJ, Bush EC, Hardin J, Wade JT, Stoebel DM. Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. J Bacteriol. 2017 Mar 14;199(7). pii: e00755-16.
  • Kasper SH, Bonocora RP, Wade JT, Musah RA, Cady NC. Chemical Inhibition of Kynureninase Reduces Pseudomonas aeruginosa Quorum Sensing and Virulence Factor Expression. ACS Chem Biol. 2016 Apr 15;11(4):1106-17.
  • Bonocora, R.P., Smith, C., Lapierre, P. and Wade, J.T. Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding. PLoS Genet. 2015 Oct 1;11(10):e1005552.
  • Fitzgerald, D.M., Bonocora, R.P. and Wade, J.T. Comprehensive mapping of the Escherichia coli flagellar regulatory network. PLoS Genet. 2014 Oct 2; 10(10):e1004649
  • Singh, S.S.*, Singh, N.*, Bonocora, R.P.*, Fitzgerald, D.M., Wade, J.T. and Grainger, D.C. Widespread suppression of intragenic transcription initiation by H-NS. Genes & Dev. 2014 Feb 1; 28(3):214-9. * Authors contributed equally.
  • Bonocora, R.P.*, Zeng, Q.*, Abel, E.V. and Shub, D.A. A homing endonuclease and the 50-nt ribosomal bypass sequence of phage T4 constitute a mobile DNA cassette. Proc Natl Acad Sci USA. 2011 Sep 27;108(39):16351-6. * Authors contributed equally.
  • Bonocora, R.P., Decker, P.K., Glass, S., Knipling, L., and Hinton, D.M. Bacteriophage T4 MotA activator and the β-flap tip of RNA polymerase target the same set of σ70 carboxyl-terminal residues. J Biol Chem. 2011 Nov 11;286(45):39290-6.
  • Bonocora, R.P. and Shub, D.A. A likely pathway for formation of mobile group I introns. Curr. Biol. 2009 Feb 10:19 223-228. (This article was the focus of a dispatch in the same issue: Edgell, D.R. Selfish DNA: Homing endonucleases fnd a home. Curr. Biol. 2009 Feb 10:19 R115-117.)