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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM088343-04S1
Application #
9079235
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Sledjeski, Darren D
Project Start
2011-04-15
Project End
2016-06-30
Budget Start
2014-04-01
Budget End
2016-06-30
Support Year
4
Fiscal Year
2015
Total Cost
$130,220
Indirect Cost
$31,065
Name
Rutgers University
Department
Type
Organized Research Units
DUNS #
001912864
City
New Brunswick
State
NJ
Country
United States
Zip Code
08901
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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
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