Richard Bonocora

Sr. 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
  • Microbiology
  • Genomics
  • Gene Regulation
  • Mobile Genetic Elements
  • Space Biology
Contact Information
Select Works
  • PM McMackin, JA Adam, SR Griffin, RP Bonocora, KA Brakke, JM Lopez & AH Hirsa. Effects of Microorganisms on Drop Formation in Microgravity During a Parabolic Flight with Residual Gravity and Jitter. Microgravity Science and Technology 34 (2), 1-9
  • Adam JA, Gulati S, Hirsa AH, Bonocora RP. Growth of microorganisms in an interfacially driven space bioreactor analog. NPJ Microgravity. 2020 Apr 8;6:11. doi: 10.1038/s41526-020-0101-4. eCollection 2020.
  • Lamberte LE, Baniulyte G, Singh SS, Stringer AM, Bonocora RP, Stracy M, Kapanidis AN, Wade JT, Grainger DC. Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nat Microbiol. 2017 Jan 9;2:16249.
  • 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. 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.)