Transcription is the first step in gene expression and the step at which most gene regulation occurs. Transcription in all cells is carried out by multi-subunit RNA polymerases (RNAPs) that are conserved in sequence, structure and function from bacteria to humans. Whereas initiation of DNA synthesis by DNA polymerase requires use of a primer, it is widely accepted that the initiation of RNA synthesis by RNAP occurs """"""""de novo"""""""" (i.e. RNAP initiates RNA synthesis using free NTPs only). With the proposed research we seek to challenge this conventional paradigm. Specifically, we will investigate the hypothesis that a significant fraction of transcription does not occur """"""""de novo"""""""", but rather relies upon use of small ~2-5 nt RNA transcripts, """"""""nanoRNAs"""""""", that influence gene expression by serving as primers to initiate transcription.
The first aim will use microarray analysis, chromatin immunoprecipitation (ChIP) coupled with fully tiled high density DNA microarrays (ChIP-on-chip), and high-throughput sequencing to define how nanoRNA- dependent priming can influence gene expression.
The second aim will use high-throughput sequencing to identify those nanoRNAs that function to prime transcription initiation in vivo.
The third aim will use microarray analysis, ChIP-on-chip, and high-throughput sequencing to determine the extent to which nanoRNA-dependent priming impacts gene expression during physiological growth conditions. The proposed research is part a long-range effort to elucidate fundamental mechanisms of gene regulation in bacteria. These studies have the potential to redefine our view of a fundamental process that occurs in all living cells (i.e. transcription) and, in parallel, uncover a novel class of regulatory small RNAs, """"""""nanoRNAs"""""""", that function in all living cells via a novel mode of action.

Public Health Relevance

In this work, we will investigate the possible existence of a novel class of regulatory small RNAs that function via a novel mode of action. Small RNAs have emerged as key regulators of cellular homeostasis as well as numerous developmental pathways and disease processes. Thus, the proposed research will lead to discoveries with important implications for pubic health.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Prokaryotic Cell and Molecular Biology Study Section (PCMB)
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Sledjeski, Darren D
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Rutgers University
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New Brunswick
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Bird, Jeremy G; Zhang, Yu; Tian, Yuan et al. (2016) The mechanism of RNA 5? capping with NAD+, NADH and desphospho-CoA. Nature 535:444-7
Vvedenskaya, Irina O; Vahedian-Movahed, Hanif; Zhang, Yuanchao et al. (2016) Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. Proc Natl Acad Sci U S A 113:E2899-905
Winkelman, Jared T; Vvedenskaya, Irina O; Zhang, Yuanchao et al. (2016) Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science 351:1090-3
Schifano, Jason M; Cruz, Jonathan W; Vvedenskaya, Irina O et al. (2016) tRNA is a new target for cleavage by a MazF toxin. Nucleic Acids Res 44:1256-70
Ramsey, Kathryn M; Osborne, Melisa L; Vvedenskaya, Irina O et al. (2015) Ubiquitous promoter-localization of essential virulence regulators in Francisella tularensis. PLoS Pathog 11:e1004793
Goldman, Seth R; Nair, Nikhil U; Wells, Christopher D et al. (2015) The primary ? factor in Escherichia coli can access the transcription elongation complex from solution in vivo. Elife 4:
Druzhinin, Sergey Y; Tran, Ngat T; Skalenko, Kyle S et al. (2015) A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq. PLoS Genet 11:e1005348
Vvedenskaya, Irina O; Goldman, Seth R; Nickels, Bryce E (2015) Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends. Methods Mol Biol 1276:211-28
Vvedenskaya, Irina O; Zhang, Yuanchao; Goldman, Seth R et al. (2015) Massively Systematic Transcript End Readout, ""MASTER"": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields. Mol Cell 60:953-65
Cruz, Jonathan W; Sharp, Jared D; Hoffer, Eric D et al. (2015) Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nat Commun 6:7480

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