Harper C, Finkenstadt, B, Woodcock, DJ, Friedrichsen, S, Semprini, S, Ashall, L, Spiller, DG, Mullins, JJ, Rand, DA, Davis, JRE & White, MRH. (2011). Dynamic Analysis of Stochastic Transcription Cycles. PLoS Biology, 9(4).
Using a novel combined experimental and theoretical approach, involving time-lapse imaging of reporter gene expression, we measured the rate of prolactin gene transcription in single pituitary cells from stable cell lines and transgenic rats. We detected regular cycles of transcriptional activity. Mathematical analysis showed that these cycles were characterized by a minimum refractory period that involved chromatin remodeling. Transcription from different reporter constructs was out-of-phase in the same cell. This work highlights the functional importance of transcription dynamics in cells.
PLoS Biology 9
Image: Thomas Vignaud [image from paper entitled: Global Human Footprint on the Linkage between Biodiversity and Ecosystem Functioning in Reef Fishes. C, Aburto-Oropeza O, Ayala Bocos A, Ayotte PM, Banks S, et al. PLoS Biol 9(4): e1000606. doi:10.1371/journal.pbio.1000606.]
Featherstone K, Harper CV, McNamara A, Semprini S, Spiller DG, McNeilly J, McNeilly AS, Mullins JJ, White MRH & Davis JRE. (2011). "Pulsatile patterns of pituitary hormone gene expression change during development" Journal of Cell Science 124, 20 3484-3491.
We used bioluminescence imaging of transgenic rat fetal and neonatal pituitary tissue to assess whether dynamic patterns of transcription change during tissue development. Gene expression in single cells was pulsatile at the time endocrine cells first appeared but became stabilised as tissue develops in early neonatal life. This stabilised transcription pattern might depend upon tissue architecture or paracrine signalling, as isolated cells. Therefore cells alter patterns of gene expression according to context and developmental stage.
Journal of Cell Science 124, 20.
Image: Reproduced with permission of Journal of Cell Science and Dr Patrick Laprise [image from paper entitled: Crumbs controls epithelial integrity by inhibiting Rac1 and PI3K. Chartier, Francois J.-M.; Hardy, Emilie J. -L.; Laprise, Patrick. Journal of Cell Science Volume: 12: Issue: 20 Pages: 3393-3398 DOI: 10.1242/jcs.092601:OCT 15 2011]
Harper CV, Featherstone K, Semprini S, Friedrichsen S, McNeilly J, Paszek P, Spiller DG, McNeilly AS, Mullins JJ, Davis JRE & White MRH. (2010) "Dynamic organisation of prolactin gene expression in living pituitary tissue" Journal of Cell Science 123, 3 424-430.
We studied coordination of transcription in single cells within living pituitary tissue compared to cells ex vivo. These studies were made possible through the establishment of transgenic rats expressing bacterial artificial chromomosomes expressing luciferase and dEGFP under the control of the human prolactin promoter. In vivo, cells were more coordinated than in isolated cells in vitro. This is important, because it shows how pituitary cell to cell communication and architecture may regulate hormone secretion in vivo.
Journal of Cell Science 123, 3.
Image: Reproduced with permission of Journal of Cell Science and Dr Lily Vardimon [image from paper entitled: Weak mitochondrial targeting sequence determines tissue-specific subcellular localization of glutamine synthetase in liver and brain cells. Gideon D. Matthews, Noa Gur, Werner J. H. Koopman, Ophry Pines & Lily Vardimon. Journal of Cell Science Volume 123 (3): 351-359. doi: 10.1242/jcs.060749: February 1, 2010.]
Spiller DG, Wood CD, Rand DA, White MRH. (2010). Measurement of single-cell dynamics. Nature, 465, 736-745.
Populations of cells are almost always heterogeneous in function and fate. To understand the plasticity of cells, it is vital to measure quantitatively and dynamically the molecular processes that underlie cell-fate decisions in single cells. Early events in cell signalling often occur within seconds of the stimulus, whereas intracellular signalling processes and transcriptional changes can take minutes or hours. By contrast, cell-fate decisions, such as whether a cell divides, differentiates or dies, can take many hours or days. Multiparameter experimental and computational methods that integrate quantitative measurement and mathematical simulation of these noisy and complex processes are required to understand the highly dynamic mechanisms that control cell plasticity and fate.
Image: Reproduced with permission of Nature Publishing Group. Image from paper entitled: Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome. Xonia Carvajal-Vergara, Ana Sevilla, Sunita L. D’Souza, Yen-Sin Ang, Christoph Schaniel, Dung-Fang Lee, Lei Yang, Aaron D. Kaplan, Eric D. Adler, Roye Rozov, YongChao Ge, Ninette Cohen, Lisa J. Edelmann, Betty Chang, Avinash Waghray, Jie Su, Sherly Pardo, Klaske D. Lichtenbelt, Marco Tartaglia, Bruce D. Gelb & Ihor R. Nature: 465, 808–812 (10 June 2010). doi:10.1038/nature09005.
Paszek P, Ryan S, Ashall L, Sillitoe K, Harper CV, Spiller DG, Rand DA & White MRH. "Population robustness arising from cellular heterogeneity" Proceedings of the National Academy of Sciences of the United States of America 107, (2010) 11644-11649.
In this paper we demonstrated the novel principle that a dual delayed negative feedback loop may control heterogeneity in NF-kappaB signalling. We showed that the IkappaBepsilon feedback loop is delayed by 45 minutes relative to IkappaBalpha and that this timing is conserved. Mathematical model analysis demonstrated that this timing lay at a theoretical optimun for generation of cell heterogeneity suggesting that heterogeneity is advantageous. We developed the novel hypothesis that this heterogeneity may minimise cytokine fluctuations in response to NF-kappaB at the tissue level. This concept is important for understanding tissue-level control of inflammation.
Proceedings of the National Academy of Sciences of the United States of America, 107.
Image: Reproduced with permission of Proceedings of the National Academy of Sciences of the United States of America. Image from paper entitled: Direct regulation of phytoene synthase gene expression and carotenoid biosynthesis by phytochrome-interacting factor. Gabriela Toledo-Ortiz, Enamul Huq, & Manuel Rodríguez-Concepción. vol. 107 no. 25 11626-1163. doi: 10.1073/pnas.091442810.
MATLAB model codes (Zip file.)
Turner DA, Paszek P, Woodcock DJ, Nelson DE, Horton CA, Wang YJ, Spiller DG, Rand DA, White MRH, Harper CV. (2010). "Physiological levels of TNF alpha stimulation induce stochastic dynamics of NF-kappa B responses in single living cells" Journal of Cell Science 123 (16) 2834-2843.
Stimulation of cells with low doses of TNFa treatment cells elicited a stochastic delay before the onset of NF-kappaB translocation and oscillations. Subsequent oscillations retain the typical 100 min period that occurs with high dose treatment. These data demonstrate the importance of single cell studies to study such a noisy and stochastic system. We used the data to refine our mathematical models of the NF-kappaB system, and this was important in providing new hypothesis about how upstream feedback loops regulate the system.
Journal of Cell Science 123, (16).
Image: Reproduced with permission of Journal of Cell Science and Martin Kracklauer [image from paper entitled: The Drosophila SUN protein Spag4 cooperates with the coiled-coil protein Yuri Gagarin to maintain association of the basal body and spermatid nucleus. Martin P. Kracklauer, Heather M. Wiora, William J. Deery, Xin Chen, Benjamin Bolival Jr, Dwight Romanowicz, Rebecca A. Simoette, Margaret T. Fuller, Janice A. Fischer & Kathleen M. Beckingham. Journal of Cell Science 123. doi: 10.1242/jcs.066589 August 15, 2010 2763-2772
Ashall L, Horton CA, Nelson DE, Paszek P, Harper CV, Sillitoe K, Ryan S, Spiller DG, Unitt JF, Broomhead DS, Kell DB, Rand DA, See V. & White MRH. (2009). Pulsatile stimulation determines timing and specificity of NF-κB-dependent transcription. Science, 324, 242-246.
We demonstrated for the first time that pulsatile TNFa control of NF-kappaB oscillation frequency controls the pattern of target gene transcription. The paper explains how cell heterogeneity may be controlled through dual negative IkappaB feedback loops. The paper had four joint first authors, two experimental and two theoretical.
Image: Robert Smock and Lila Gierasch. From Science 10 April 2009:Vol. 324 o. 5924. Reprinted with permission from AAAS.
MATLAB model codes (Zip file.)
Nelson D, Ihekwaba A, Elliott M, Johnson J, Gibney C, Foreman B, Nelson G, See V, Horton C, Spiller D, Edwards S, McDowell H, Unitt J, Sullivan E, Grimley R, Benson N, Broomhead D, Kell D & White, M. (2004). Oscillations in NF-kappa B signaling control the dynamics of gene expression. Science 306: 704-8
Signaling by the transcription factor nuclear factor kappa B (NF-kappaB) involves its release from inhibitor kappa B (IkappaB) in the cytosol, followed by translocation into the nucleus. NF-kappaB regulation of IkappaBalpha transcription represents a delayed negative feedback loop that drives oscillations in NF-kappaB translocation. Single-cell time-lapse imaging and computational modeling of NF-kappaB (RelA) localization showed asynchronous oscillations following cell stimulation that decreased in frequency with increased IkappaBalpha transcription. Transcription of target genes depended on oscillation persistence, involving cycles of RelA phosphorylation and dephosphorylation. The functional consequences of NF-kappaB signaling may thus depend on number, period & amplitude of oscillations.
Image: Myriam Kirkman-O. From Science 22 October 2004 vol 306, issue 569. Reprinted with permission from AAAS.