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 alone). The proposed research will 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 that serve as primers to initiate transcription. We refer to these ~2-5 nt RNA transcripts as "nanoRNAs". According to our model, the cell balances nanoRNA-primed transcription and de novo transcription to maintain cellular homeostasis. Furthermore, celular perturbations that alter the balance betwen nanoRNA-primed transcription and de novo transcription lead to global alterations in gene expression. Consistent with this model, we have found that increasing the intracellular concentration of nanoRNAs leads to global alterations in gene expression coupled with an apparent increase in the occurrence of nanoRNA-primed transcription. Building on these findings, we propose to use genetic and biochemical approaches in conjunction with high- throughput sequencing to determine how nanoRNA priming can alter gene expression, identify factors that control the nanoRNA content of the cell, and systematically identify nanoRNAs. The proposed research has 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

The proposed work will investigate the existence of a novel class of regulatory small RNAs, nanoRNAs, 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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM096454-04
Application #
8529562
Study Section
Special Emphasis Panel (ZRG1-BCMB-A (51))
Program Officer
Sledjeski, Darren D
Project Start
2010-09-30
Project End
2015-08-31
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
4
Fiscal Year
2013
Total Cost
$747,516
Indirect Cost
$130,652
Name
Rutgers University
Department
None
Type
Organized Research Units
DUNS #
001912864
City
New Brunswick
State
NJ
Country
United States
Zip Code
08901
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
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
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
Goldman, Seth R; Nair, Nikhil U; Wells, Christopher D et al. (2015) The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo. Elife 4:
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
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
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
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; Vahedian-Movahed, Hanif; Bird, Jeremy G et al. (2014) Interactions between RNA polymerase and the "core recognition element" counteract pausing. Science 344:1285-9
Vvedenskaya, Irina O; Sharp, Josh S; Goldman, Seth R et al. (2012) Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. Genes Dev 26:1498-507

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