Skip Navigation

Nucleic Acids Research 2004 32(20):e160; doi:10.1093/nar/gnh157
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (287K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Jacobs, J. L.
Right arrow Articles by Dinman, J. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jacobs, J. L.
Right arrow Articles by Dinman, J. D.
Related Collections
Right arrow Monitoring gene expression
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 23 November 2004

Nucleic Acids Research, Vol. 32 No. 20 © Oxford University Press 2004; all rights reserved

Systematic analysis of bicistronic reporter assay data

Jonathan L. Jacobs and Jonathan D. Dinman*

Department of Cell Biology and Molecular Genetics, 2135 Microbiology Building, University of Maryland, College Park, MD 20742, USA

* To whom correspondence should be addressed. Tel: +1 301 405 0918; Fax: +1 301 314 9489; Email: dinman{at}umd.edu

Received August 12, 2004; Revised October 6, 2004; Accepted October 29, 2004

Bicistronic reporter assay systems have become a mainstay of molecular biology. While the assays themselves encompass a broad range of diverse and unrelated experimental protocols, the numerical data garnered from these experiments often have similar statistical properties. In general, a primary dataset measures the paired expression of two internally controlled reporter genes. The expression ratio of these two genes is then normalized to an external control reporter. The end result is a ‘ratio of ratios’ that is inherently sensitive to propagation of the error contributed by each of the respective numerical components. The statistical analysis of this data therefore requires careful handling in order to control for the propagation of error and its potentially misleading effects. A careful survey of the literature found no consistent method for the statistical analysis of data generated from these important and informative assay systems. In this report, we present a detailed statistical framework for the systematic analysis of data obtained from bicistronic reporter assay systems. Specifically, a dual luciferase reporter assay was employed to measure the efficiency of four programmed –1 frameshift signals. These frameshift signals originate from the L-A virus, the SARS-associated Coronavirus and computationally identified frameshift signals from two Saccharomyces cerevisiae genes. Furthermore, these statistical methods were applied to prove that the effects of anisomycin on programmed –1 frameshifting are statistically significant. A set of Microsoft Excel spreadsheets, which can be used as templates for data generated by dual reporter assay systems, and an online tutorial are available at our website (http://dinmanlab.umd.edu/statistics). These spreadsheets could be easily adapted to any bicistronic reporter assay system.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
P.-Y. Liao, Y. S. Choi, and K. H. Lee
FSscan: a mechanism-based program to identify +1 ribosomal frameshift hotspots
Nucleic Acids Res., September 26, 2009; (2009) gkp796v1.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
T. S. Cardno, E. S. Poole, S. F. Mathew, R. Graves, and W. P. Tate
A homogeneous cell-based bicistronic fluorescence assay for high-throughput identification of drugs that perturb viral gene recoding and read-through of nonsense stop codons
RNA, August 1, 2009; 15(8): 1614 - 1621.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. N. Petrov, A. Meskauskas, S. C. Roshwalb, and J. D. Dinman
Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit
Nucleic Acids Res., November 1, 2008; 36(19): 6187 - 6198.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P.-Y. Liao, P. Gupta, A. N. Petrov, J. D. Dinman, and K. H. Lee
A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting
Nucleic Acids Res., May 1, 2008; 36(8): 2619 - 2629.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Meskauskas, J. R. Russ, and J. D. Dinman
Structure/function analysis of yeast ribosomal protein L2
Nucleic Acids Res., April 1, 2008; 36(6): 1826 - 1835.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Rakauskaite and J. D. Dinman
rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance
Nucleic Acids Res., March 1, 2008; 36(5): 1497 - 1507.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
O. Galkin, A. A. Bentley, S. Gupta, B.-A. Compton, B. Mazumder, T. G. Kinzy, W. C. Merrick, M. Hatzoglou, T. V. Pestova, C. U.T. Hellen, et al.
Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5
RNA, December 1, 2007; 13(12): 2116 - 2128.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. L. Jacobs, A. T. Belew, R. Rakauskaite, and J. D. Dinman
Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae
Nucleic Acids Res., January 12, 2007; 35(1): 165 - 174.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
R. Rakauskaite and J. D. Dinman
An Arc of Unpaired "Hinge Bases" Facilitates Information Exchange among Functional Centers of the Ribosome
Mol. Cell. Biol., December 1, 2006; 26(23): 8992 - 9002.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
K. L. Muldoon-Jacobs and J. D. Dinman
Specific effects of ribosome-tethered molecular chaperones on programmed -1 ribosomal frameshifting.
Eukaryot. Cell, April 1, 2006; 5(4): 762 - 770.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
A. Meskauskas, A. N. Petrov, and J. D. Dinman
Identification of Functionally Important Amino Acids of Ribosomal Protein L3 by Saturation Mutagenesis
Mol. Cell. Biol., December 15, 2005; 25(24): 10863 - 10874.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
D. S. McNabb, R. Reed, and R. A. Marciniak
Dual Luciferase Assay System for Rapid Assessment of Gene Expression in Saccharomyces cerevisiae
Eukaryot. Cell, September 1, 2005; 4(9): 1539 - 1549.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.