A critical control point for regulating gene expression in eukaryotic cells is during mRNA transcription by RNA polymerase II (Pol II). Non-coding RNA molecules (ncRNAs) have emerged as a new class of transcriptional regulators in a variety of cellular systems. 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 research funded by the parent grant is to understand how mammalian ncRNAs that bind to Pol II control transcription in biologically important and medically relevant experimental systems. The proposed work will complement and extend the goals of the parent grant by identifying and investigating new ncRNA/Pol II complexes in cells. Doing so will test the hypothesis that Pol II contains a high-affinity docking site for ncRNAs, and that diverse ncRNAs bind this site and function as trans-regulators of Pol II transcription in different cellular systems. The proposal hs one Specific Aim: Identify and characterize novel ncRNA/Pol II complexes that form under distinct cellular conditions. New macromolecular complexes containing ncRNAs and Pol II will be found by immunoprecipitating Pol II and sequencing the associated RNAs. Two cellular systems will be used, one focusing on a program of differentiation and the other on cell cycle progression. For selected ncRNAs the percent of each ncRNA bound to Pol II, and how this changes under different conditions and cell types, will be experimentally determined. In addition, the contribution the selected ncRNAs make to the overall programs of differentiation and cell cycle progression in the two cell types will be investigated. These studies will move the fields o transcriptional regulation and functional ncRNAs in new directions. A new class of macromolecular complexes in cells will be defined that have potential to control gene expression through novel mechanisms. Results from the proposed work will provide the platform for future lines of research that will investigate how ncRNAs that complex with Pol II control transcriptional activity during programs of cellular differentiation and cell cycle progression.

Public Health Relevance

Properly controlling gene expression is essential to sustaining life and avoiding many diseases and cancers;mRNA transcription by RNA polymerase II (Pol II) is central to this process. These studies will identify new macromolecular complexes between Pol II and non-coding RNAs that form during specific programs of differentiation and cell cycle progression. Acquiring this knowledge could reveal novel mechanisms of cellular regulation that have the potential to be widespread.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-CBB-0 (MI))
Program Officer
Sledjeski, Darren D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Colorado at Boulder
Schools of Arts and Sciences
United States
Zip Code
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
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
Wagner, Stacey D; Yakovchuk, Petro; Gilman, Benjamin et al. (2013) RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. EMBO J 32:781-90
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 (2012) Non-coding RNAs: key regulators of mammalian transcription. Trends Biochem Sci 37:144-51

Showing the most recent 10 out of 24 publications