Transcriptional Bursting in Confined Cell-Free Reactions
- Conference: Synthetic Biology Engineering Evolution Design SEED
- Year: 2015
- Proceeding: 2015 Synthetic Biology: Engineering, Evolution & Design (SEED)
- Group: Poster Session
Friday, June 12, 2015 - 5:15pm-6:45pm
Microsoft Word - SEED 2015 abstract Caveney.docx
Transcriptional Bursting in Confined Cell-Free Reactions
Patrick M. Caveney1,2, Sarah E. Norred1,2, Charles Chin1,2, Scott T. Retterer1,2, Charles P. Collier2,
Michael L. Simpson1,2,3
1Bredesen Center, University of Tennessee Knoxville, 2Center for Nanophase Materials Sciences, Oak Ridge
National Laboratory, 3Department of Materials Science and Engineering, University of Tennessee Knoxville
Transcriptional bursting, bursts of transcription followed by periods of inactivity, is widely observed across all life1,2,3,4,5,6,7. This phenomenon is important for many cell fate decisions such as proviral latency in HIV8,9,10,11,12. The widely studied two-state (or random telegraph) model is
characterized by the transitions between ON and OFF, kON and kOFF respectively
mechanisms have been proposed including: supercoiling19, transcription factor kinetics20, chromatin
remodeling21,22, and transcriptional reinitiation23,24,25. However, these studies neglect spatial
correlations caused by in vivo crowding (40%26) and confinement (~10 femtoliters)27,28 that may
contribute to transcriptional bursting29,30. We present experimental and simulation evidence of
transcriptional bursting in confined cell-free protein synthesis reactions absent the proposed molecular mechanisms of bursting. And demonstrate that the magnitude and dynamics of bursting may be manipulated by control of confinement.
1. Blake, William J., Mads KÃ¦rn, Charles R. Cantor, and James J. Collins. "Noise in eukaryotic gene
expression." Nature 422, no. 6932 (2003): 633-637.
2. Skupsky, Ron, John C. Burnett, Jonathan E. Foley, David V. Schaffer, and Adam P. Arkin. "HIV promoter integration site primarily modulates transcriptional burst size rather than frequency." PLoS computational biology 6, no. 9 (2010): e1000952.
3. Taniguchi, Yuichi, Paul J. Choi, Gene-Wei Li, Huiyi Chen, Mohan Babu, Jeremy Hearn, Andrew Emili, and X.
Sunney Xie. "Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells." Science 329, no. 5991 (2010): 533-538.
4. Dar, Roy D., Brandon S. Razooky, Abhyudai Singh, Thomas V. Trimeloni, James M. McCollum, Chris D. Cox,
Michael L. Simpson, and Leor S. Weinberger. "Transcriptional burst frequency and burst size are equally modulated across the human genome." Proceedings of the National Academy of Sciences 109, no. 43 (2012): 17454-
5. Hensel, Zach, Haidong Feng, Bo Han, Christine Hatem, Jin Wang, and Jie Xiao. "Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis." Nature structural & molecular biology 19, no. 8 (2012): 797-802.
6. Levine, Joe H., Yihan Lin, and Michael B. Elowitz. "Functional roles of pulsing in genetic circuits." Science 342, no. 6163 (2013): 1193-1200.
7. Carey, Lucas B., David Van Dijk, Peter MA Sloot, Jaap A. Kaandorp, and Eran Segal. "Promoter sequence determines the relationship between expression level and noise." PLoS biology 11, no. 4 (2013): e1001528.
8. Weinberger, Leor S., John C. Burnett, Jared E. Toettcher, Adam P. Arkin, and David V. Schaffer. "Stochastic
gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity." Cell 122, no. 2 (2005): 169-182.
9. Weinberger, Leor S., and Thomas Shenk. "An HIV feedback resistor: auto-regulatory circuit deactivator and
noise buffer." PLoS biology 5, no. 1 (2006): e9.
10. Weinberger, Leor S., Roy D. Dar, and Michael L. Simpson. "Transient-mediated fate determination in a transcriptional circuit of HIV." Nature genetics 40, no. 4 (2008): 466-470.
11. Dar, Roy D., Brandon S. Razooky, Abhyudai Singh, Thomas V. Trimeloni, James M. McCollum, Chris D. Cox, Michael L. Simpson, and Leor S. Weinberger. "Transcriptional burst frequency and burst size are equally
modulated across the human genome." Proceedings of the National Academy of Sciences 109, no. 43 (2012): 17454-
12. Weinberger, Ariel D., and Leor S. Weinberger. "Stochastic fate selection in HIV-infected patients." Cell 155, no.
3 (2013): 497-499.
13. Kepler, Thomas B., and Timothy C. Elston. "Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations."Biophysical journal 81, no. 6 (2001): 3116-3136.
14. Simpson, Michael L., Chris D. Cox, and Gary S. Sayler. "Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation."Journal of theoretical biology 229, no. 3 (2004): 383-394.
15. Paulsson, Johan. "Models of stochastic gene expression." Physics of life reviews 2, no. 2 (2005): 157-175.
16. Pedraza, Juan M., and Johan Paulsson. "Effects of molecular memory and bursting on fluctuations in gene expression." Science 319, no. 5861 (2008): 339-343.
17. Elgart, Vlad, Tao Jia, and Rahul V. Kulkarni. "Applications of Littleâ??s Law to stochastic models of gene expression." Physical Review E 82, no. 2 (2010): 021901.
18. Jia, Tao, and Rahul V. Kulkarni. "Post-transcriptional regulation of noise in protein distributions during gene expression." Physical review letters 105, no. 1 (2010): 018101.
19. Chong, Shasha, Chongyi Chen, Hao Ge, and X. Sunney Xie. "Mechanism of transcriptional bursting in
bacteria." Cell 158, no. 2 (2014): 314-326.
20. Bialek, William, and Sima Setayeshgar. "Physical limits to biochemical signaling." Proceedings of the National
Academy of Sciences of the United States of America 102, no. 29 (2005): 10040-10045.
21. Raj, Arjun, Patrick Van Den Bogaard, Scott A. Rifkin, Alexander Van Oudenaarden, and Sanjay Tyagi. "Imaging individual mRNA molecules using multiple singly labeled probes." Nature methods 5, no. 10 (2008):
22. Raser, Jonathan M., and Erin K. O'Shea. "Control of stochasticity in eukaryotic gene expression." Science 304, no. 5678 (2004): 1811-1814.
23. Golding, Ido, Johan Paulsson, Scott M. Zawilski, and Edward C. Cox. "Real-time kinetics of gene activity in individual bacteria." Cell 123, no. 6 (2005): 1025-1036.
24. Zenklusen, Daniel, Daniel R. Larson, and Robert H. Singer. "Single-RNA counting reveals alternative modes of
gene expression in yeast." Nature structural & molecular biology 15, no. 12 (2008): 1263-1271.
25. Blake, William J., Mads KÃ¦rn, Charles R. Cantor, and James J. Collins. "Noise in eukaryotic gene expression." Nature 422, no. 6932 (2003): 633-637.
26. Zimmerman, Steven B., and Stefan O. Trach. "Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli." Journal of molecular biology 222, no. 3 (1991): 599-620.
27. Tan, Cheemeng, Saumya Saurabh, Marcel P. Bruchez, Russell Schwartz, and Philip LeDuc. "Molecular crowding shapes gene expression in synthetic cellular nanosystems." Nature nanotechnology 8, no. 8 (2013): 602-
28. Fowlkes, Jason D., and C. Patrick Collier. "Single-molecule mobility in confined and crowded femtolitre chambers." Lab on a Chip 13, no. 5 (2013): 877-885.
29. Meyer, B., E. Agliari, O. BÃ©nichou, and R. Voituriez. "Exact calculations of first-passage quantities on recursive networks." Physical Review E 85, no. 2 (2012): 026113.
30. van Zon, Jeroen S., Marco J. Morelli, Sorin TÇ?nase-Nicola, and Pieter Rein ten Wolde. "Diffusion of
transcription factors can drastically enhance the noise in gene expression." Biophysical journal 91, no. 12 (2006):