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Faculty Highlight: Richard Bonocora

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.