A critical control point for regulating gene expression in eukaryotic cells is during mRNA transcription by RNA polymerase II (Pol II). Unexpectedly, non-coding RNA molecules (ncRNAs) have been found to regulate mRNA transcription. Mouse B2 RNA and human Alu RNA are two such ncRNAs;they function as repressors of mRNA transcription by binding directly to Pol II in response to heat shock, a widely used model system for studying the cellular stress response. The long term goal of this research is to understand how mammalian ncRNAs directly control Pol II transcription in biologically important and medically relevant experimental systems. These studies will contribute to discerning how transcription is regulated during cellular stress, which is critical for understanding abnormalities in gene expression associated with diseases and deleterious environmental states. Moreover, our studies will move the fields of transcriptional regulation and functional ncRNAs in new directions. The proposal has three Specific Aims. 1) Determine how B2 RNA controls genome-wide Pol II occupancy and the molecular characteristics of paused complexes in response to heat shock using a combination of genomic assays (e.g. ChIP-seq, RNA-seq) and more targeted assays (e.g. ChIP, permanganate treatment). 2) Identify and study factors that control the activities of B2 RNA and Alu RNA using in vitro protein-RNA interaction assays, cellular knockdown of factors, co-immunoprecipitations, and ChIP. 3) Understand the mechanism and functions of the mammalian Pol II RdRP activity using a combination of RdRP assays, RNA secondary structure analysis, protein-RNA interaction assays, in vitro transcription experiments, and targeted RNA-seq. Together this work will contribute a new understanding of how ncRNAs can globally regulate a critical biological process. Moreover, by using as a model system the widespread, yet transient, transcriptional repression that occurs in response to heat shock, we are uniquely poised to uncover new aspects of transcriptional control of macromolecular complex assembly on promoters and post-initiation events. In addition, we will identify and characterize a global regulator of transcriptional activation in response to heat shock that functions by derepressing the activities of B2 and Alu RNAs. Lastly, our experiments will be the first to characterize mammalian Pol II as an RdRP that acts on cellular RNA templates.

Public Health Relevance

Properly controlling gene expression is essential to sustaining life and avoiding many diseases and cancers;mRNA transcription by RNA polymerase II is central to this process. The proposed studies will define a new means by which programs of mRNA transcription are controlled during cellular stress. Acquiring this knowledge is critical for understanding abnormalities in gene expression associated with diseases and deleterious environmental states.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-GGG-N (03))
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Sledjeski, Darren D
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University of Colorado at Boulder
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Cardiello, Joseph F; Goodrich, James A; Kugel, Jennifer F (2018) Heat Shock Causes a Reversible Increase in RNA Polymerase II Occupancy Downstream of mRNA Genes, Consistent with a Global Loss in Transcriptional Termination. Mol Cell Biol 38:
Goodrich, James; Taatjes, Dylan (2018) Transcription regulation enters a new phase. Nature 558:197-198
Kugel, Jennifer F; Goodrich, James A (2017) Finding the start site: redefining the human initiator element. Genes Dev 31:1-2
Eidem, Tess M; Kugel, Jennifer F; Goodrich, James A (2016) Noncoding RNAs: Regulators of the Mammalian Transcription Machinery. J Mol Biol 428:2652-2659
Goodrich, James A; Kugel, Jennifer F (2015) Studying the affinity, kinetic stability, and specificity of RNA/protein interactions: SINE ncRNA/Pol II complexes as a model system. Methods Mol Biol 1206:165-78
Abrisch, Robert G; Eidem, Tess M; Yakovchuk, Petro et al. (2015) Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. J Virol 90:2503-13
Ponicsan, Steven L; Kugel, Jennifer F; Goodrich, James A (2015) Repression of RNA Polymerase II Transcription by B2 RNA Depends on a Specific Pattern of Structural Regions in the RNA. Noncoding RNA 1:4-16
Kassube, Susanne A; Fang, Jie; Grob, Patricia et al. (2013) Structural insights into transcriptional repression by noncoding RNAs that bind to human Pol II. J Mol Biol 425:3639-48
Kugel, Jennifer F; Goodrich, James A (2013) The regulation of mammalian mRNA transcription by lncRNAs: recent discoveries and current concepts. Epigenomics 5:95-102
Ponicsan, Steven L; Houel, Stephane; Old, William M et al. (2013) The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II. J Mol Biol 425:3625-38

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